James Fellows Yates (james_fellows_yates@eva.mpg.de)
2019-10-28 20:44:54

@James Fellows Yates has joined the channel

Åshild (Ash) (ashild.v@gmail.com)
2019-10-28 20:49:46

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Anna F. (annakfos@gmail.com)
2019-10-28 21:00:45

@Anna F. has joined the channel

ivelsko (velsko@shh.mpg.de)
2019-10-28 21:40:38

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Alex Hübner (alexander_huebner@eva.mpg.de)
2019-10-29 09:01:26

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Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2019-10-29 10:13:34

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invite-slack (jfy133@gmail.com)
2020-02-05 05:40:57

@invite-slack has joined the channel

Zandra Fagernäs (fagernaes@shh.mpg.de)
2020-02-05 14:40:56

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Miriam Bravo (bravolomiriam@gmail.com)
2020-02-05 19:01:20

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aidanva (aida.andrades@gmail.com)
2020-03-04 15:20:04

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Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-03-12 05:37:37

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Jaelle Brealey (jcbrealey@gmail.com)
2020-03-12 09:01:56

@Jaelle Brealey has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-03-12 10:33:06

Hello @channel nice to see the slack link is working!

Emrah Kırdök (emrahkirdok@gmail.com)
2020-03-12 13:58:28

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Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-03-12 15:12:32

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Pooja Swali (swalipooja@gmail.com)
2020-03-12 16:19:29

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Sterling Wright (sterlingwright2016@utexas.edu)
2020-03-23 14:54:38

@Sterling Wright has joined the channel

Ele (eg715@york.ac.uk)
2020-03-28 10:42:56

@Ele has joined the channel

Nico Rascovan (nicorasco@gmail.com)
2020-05-25 14:48:53

@Nico Rascovan has joined the channel

Maxime Borry (maxime.borry@gmail.com)
2020-05-25 19:06:12

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Maria Spyrou (spyrou@shh.mpg.de)
2020-05-25 19:19:34

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James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-08-31 20:25:03

@channel some small updates:

1) Provisional schedule can be seen here: https://spaam-workshop.github.io/#/spaam2/programme (this will be updated over time), note the shift to afternoon/evening to accommodate the Americas 2) Session abstracts will be sent out in a week or so to help you get an idea what we will cover

spaam-workshop.github.io
Åshild (Ash) (ashild.v@gmail.com)
2020-09-14 17:14:11

@channel I’ve re-sent an email that I circulated to everyone last week since it ended up in several people’s spam folders again. Here is the contents of that email in case someone has missed it:

> Dear all, > > We are pleased to announce that the schedule, as well as session and icebreaker abstracts, for SPAAM2 are now available online (https://spaam-workshop.github.io/#/spaam2/programme, subject to minor changes!). > > SPAAM2 sessions will be held virtually on the 21st and 22nd September from 13:00 to 20:00 CEST. > > The discussion sessions will be hosted on Zoom. For those who can only listen in, this will either be hosted via Zoom (muted) or private Youtube live stream. Links and passwords will be sent on Friday 18th September via email prior to the event (please keep an eye on your junk folder). A live chat will be hosted in our slack workspace under the channel <#CPHECT30A|spaam2-open> (invite link here: https://spaam-workshop.github.io/#/?id=standards-precautions-and-advances-in-metagenomics), here all members can have parallel discussions and listener-only attendees can ask a (limited) number of questions. Please let us know if you will not be able to attend. > > In cases where it would be feasible and in accordance with the current COVID-19 guidelines for your countries/institutions, we suggest participants from the same lab-group join the meeting together on a shared call. This is to minimise the number of drop-outs in case of bad internet connections. > > We would also like to remind you that by joining any of the livestreams, you will be by default agreeing to the code of conduct, which can be found on the website (https://spaam-workshop.github.io/#/spaam2/codeofconduct). > > We would also like to circulate a list of the participants including names and affiliations to those participating in the discussions. Please reply to this email or message a member of the organizing committee on Slack to let us know if you DO NOT consent to having your name and affiliation circulated to other participants. > > Kind regards, > > Åshild Vågene, James Fellows Yates & the SPAAM2 organising committee

spaam-workshop.github.io
spaam-workshop.github.io
spaam-workshop.github.io
👍 James Fellows Yates, Shreya, Nikolay Oskolkov, Emrah Kırdök
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:16:39

I wonder if someone else should send it as well, in case it address is blacklisted (ffs email sucks so much nowadays)

Åshild (Ash) (ashild.v@gmail.com)
2020-09-14 17:17:59

*Thread Reply:* I used my university email this time instead of my gmail, hopefully it should reach people now. Those who’s junk it ended up in all had uni emails

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:18:24

*Thread Reply:* Ahhh ok

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:18:32

*Thread Reply:* Hopefully that helps

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:18:58

*Thread Reply:* Although it is ridiculous that I get more 'spam' from institutional emails then Gmail 😂

Åshild (Ash) (ashild.v@gmail.com)
2020-09-14 17:19:07

*Thread Reply:* Hopefully! If not, I hope people check the website

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:19:22

*Thread Reply:* Ooh we should tweet too!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:19:26

*Thread Reply:* Completely forgot

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:19:46

*Thread Reply:* I'm on my phone with Maia at the park, maybe you could draft one?

Åshild (Ash) (ashild.v@gmail.com)
2020-09-14 17:19:47

*Thread Reply:* Yes, please do and we can retweet

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:20:02

*Thread Reply:* Uhh ok I can also try

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:27:14

*Thread Reply:* Done: https://twitter.com/jafellowsyates/status/1305528478134132736?s=19

twitter
} James Fellows Yates (https://twitter.com/jafellowsyates/status/1305528478134132736)
Åshild (Ash) (ashild.v@gmail.com)
2020-09-14 17:33:49

*Thread Reply:* sorry, didn’t see in time

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:36:39

*Thread Reply:* No problem, my mum took over

💪 Åshild (Ash)
😊 Betsy Nelson
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-14 17:38:18

For those who are Twitter inclined: https://spaam-community.slack.com/archives/CPHECT30A/p1600097234008300?threadts=1600096599.006000&cid=CPHECT30A|https://spaam-community.slack.com/archives/CPHECT30A/p1600097234008300?threadts=1600096599.006000&cid=CPHECT30A

} James Fellows Yates (https://spaam-community.slack.com/team/UPVPSB7V2)
Åshild (Ash) (ashild.v@gmail.com)
2020-09-18 17:43:33

@channel Here come the details for the meeting next week, in case you didn’t get either of my two emails that I just sent (check your spaam folders)

```Hi everyone, (sending twice from different accounts so everyone gets it)

Below is the zoom registration link for the Standards, Precautions & Advances in Ancient Metagenomics 2 discussion workshop taking place next week on Monday 21st and Tuesday 22nd September between 1-8PM CEST. A zoom instruction manual and overview of how the meeting will function is attached (i.e. who can ask questions and how). Attached is also a list of the participants.

You are invited to a Zoom meeting. When: Sep 21, 2020 12:30 PM Copenhagen & Sep 22, 2020 12:30 PM Copenhagen

Register in advance for this meeting:

https://ucph-ku.zoom.us/meeting/register/u5Iqf-mvqTkjEtTmZHwqX9o1xht_p789LBgF

After registering, you will receive a confirmation email with the zoom link. This link will be active on both days between the times 12:30-8PM CEST.

As you enter the meeting we will add either (discussant) or (listener) to the end of your zoom name. Discussants will be able to have their video on and have full control of their microphones. Listeners will not be able to turn on their video or unmute themselves and must ask questions in either the Slack channel (#spaam2-open) or zoom chat (see attached How-to for further details).

Each session will start with one or several icebreaker talks about topics that are intended to act as primers for the following discussions. Please see the programme (note the new URL!) for a reminder of the sessions and icebreakers: https://spaam-community.github.io/#/spaam2/programme

We would also like your input! Please let us know ASAP via slack or email if there are any topics that you would like to be discussed. We will not have a set agenda for the discussions, but will have a slide(s) with a list of relevant topics/issues for each session that we can draw upon if people are feeling shy ;). We would like to add any suggestions you have to these slides. Please indicate a relevant session your question/topic could be talked about. We will also try to avoid discussions of one topic lasting for too long.

Additionally, in the last few days we have had a lot of last-minute requests from people who want to listen in/watch. However, since this is not a normal conference, but a discussion-based workshop where we encourage participation from people (particularly PhDs and postdocs) who are actively doing the research, we, the organizers, have decided not to allow further participants as we are already 77 people (38 discussants and ~39 listeners).

If you know someone who would like to listen-in we will allow them to share your stream (if the current covid-19 guidelines in your area allows this).

We will be removing meeting registrants whose names do not match up with the participant list attached.

See you on Monday!

The Organization Team Standards, Precautions & Advances in Ancient Metagenomics 2```

Åshild (Ash) (ashild.v@gmail.com)
2020-09-18 17:43:58
Åshild (Ash) (ashild.v@gmail.com)
2020-09-21 10:01:01

@James Fellows Yates Is the sky blue in Jena? (test)

👍 James Fellows Yates, Clio Der Sarkissian
🤔 James Fellows Yates
B01AHATEVMG
2020-09-21 13:39:44

Did I understand how polls work?

ivelsko (velsko@shh.mpg.de)
2020-09-21 13:45:02

sorry technical issues!

Anna F. (annakfos@gmail.com)
2020-09-21 13:51:37

@channel - please feel free to change the ‘View’ setting on your zoom - on the top right corner. You can change is so you can see the presentation speaker alongside the presentation etc

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:05:44

@channel any questions or comments for Zandra or Jaelle specifically?

Vilma Perez (vilma.perez@adelaide.edu.au)
2020-09-21 14:07:01

I am working with soil samples and there isn't much that we can do to minimise the contamination. Any thoughts about that?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:07:35

*Thread Reply:* Will get to that after Irina's initial discussions

Vilma Perez (vilma.perez@adelaide.edu.au)
2020-09-21 14:09:03

*Thread Reply:* thanks!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:09:35

*Thread Reply:* Probably discussion points 2

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:13:12
B01AHATEVMG
2020-09-21 14:14:47

Who is working in the web lab?

B01AHATEVMG
2020-09-21 14:21:39

I upload my blanks

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:28:12

Depending on your sequencing centre, you might not be able to track down index hopping, if the indices have been removed as part of pre-processing by the centre

B01AHATEVMG
2020-09-21 14:28:27

Does your lab sequence on HiSeq 4000

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:28:36

It works well if you have in-line barcodes. Then quantification of index hopping is easy

👍 James Fellows Yates, Jaelle Brealey
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:31:31

Sooooooooooooooooooooooooo you guys were too enthusatic in voting and so I'm going to change polling app.

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:31:47

Should we sequence all the blanks? Or only 1 per batch (we are usually having 2)?

👍 James Fellows Yates
Polly
2020-09-21 14:32:13

@James Fellows Yates has a poll for you!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:33:39

OK the poll also reads markdown 🤦 The second '2' is meant to be \>2

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:33:43

(more than)

Åshild (Ash) (ashild.v@gmail.com)
2020-09-21 14:34:29

It depends on the size of the batch

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:34:31

What about library prep blanks? Sequence those? How many per lib prep batch?

Åshild (Ash) (ashild.v@gmail.com)
2020-09-21 14:34:48

1 extraction + 1 lib blank per 10 samples usually

👍 Ele, Katerina Guschanski, Lena G, Anna F., Betsy Nelson
Ele (eg715@york.ac.uk)
2020-09-21 14:35:06

*Thread Reply:* Same for me

Meriam Guellil (meriam.guellil.ac@gmail.com)
2020-09-21 14:35:07

*Thread Reply:* that's what I used to do as well

Jessica Hider (hiderj@mcmaster.ca)
2020-09-21 14:39:02

*Thread Reply:* Poinar lab too typically

Polly
2020-09-21 14:42:01

@James Fellows Yates has a poll for you!

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:45:57

We work with historical samples: not old enough to have a lot of damage. We are really happy about any damage we find to use for authentication

👍 Åshild (Ash), Anna F.
Polly
2020-09-21 14:51:30

@James Fellows Yates has a poll for you!

Jessica Hider (hiderj@mcmaster.ca)
2020-09-21 14:51:38

We tend to sequence deeper as far as I know (I did this), and we've been playing with bioinformatic ways of dealing with damage

👍 Anna F., Adrian Forsythe
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:54:25

Wouldn't sequencing blanks in a separate run create additional batch effects?

😀 Jessica Hider
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:55:20

*Thread Reply:* You'd think ;). But the reason why we ended up doing that because we had leaking of capture libraries into blanks

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 14:55:41

*Thread Reply:* And people got very Paranoid

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:56:26

*Thread Reply:* Ah, makes sense. With in-line barcodes that's not a problem. They have other problems, though, like reduced ligation efficiency depending on the barcode sequence

👍 James Fellows Yates
Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-09-21 14:55:58

I hadn't heard of internal barcodes until now...

Maria Zicos (m.zicos@qmul.ac.uk)
2020-09-21 14:56:17

*Thread Reply:* I have, but still feel very fuzy about them!

Polly
2020-09-21 14:56:19

@James Fellows Yates has a poll for you!

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 14:58:10

Please note that there are ligation biases with internal barcodes. Check out Brealey et al. 2020 MBE

👍 Becky Cribdon, Åshild (Ash), Jaelle Brealey
Ele (eg715@york.ac.uk)
2020-09-21 14:59:03

*Thread Reply:* Awesome thanks! Could you please link the paper?

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 15:00:04
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-21 15:00:19

*Thread Reply:* I think the barcode bias discussion is in the supp

Jaelle Brealey (jaelle.brealey@ntnu.no)
2020-09-21 15:01:14

*Thread Reply:* Yes, we had to move it out of the main text so it's completely in the Supp Info document

Ele (eg715@york.ac.uk)
2020-09-21 15:32:16

*Thread Reply:* Brilliant - thanks so much 😄

Nico Rascovan (nicorasco@gmail.com)
2020-09-21 15:42:06

Related to the genotyping and the issue of using just a single reference genome, there is this paper from last week that propose a nice turnarround by mapping into graphs rather than genomes... https://pubmed.ncbi.nlm.nih.gov/32943086/

PubMed
👍 Jaelle Brealey, Åshild (Ash), Kun Huang, Susanna Sabin, Betsy Nelson
👍:skin_tone_4: Miriam Bravo, Anna F.
Nico Rascovan (nicorasco@gmail.com)
2020-09-21 15:42:23

Using this in the framework of ancient microbes could be quite interesting

Maxime Borry (maxime.borry@gmail.com)
2020-09-21 15:45:07

*Thread Reply:* I was going to ask a question about this very paper 🙂

aidanva (aida.andrades@gmail.com)
2020-09-21 15:42:39

I agree

Åshild (Ash) (ashild.v@gmail.com)
2020-09-21 15:42:53

yup

Kun Huang (kun.huang@unitn.it)
2020-09-21 15:43:19

variation graph is a very a cool idea

ivelsko (velsko@shh.mpg.de)
2020-09-21 15:45:28

I think this is the Hungarian mummy paper: https://www.nature.com/articles/ncomms7717

Nature Communications
Åshild (Ash) (ashild.v@gmail.com)
2020-09-21 15:46:17
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 15:50:30

@Kun Huang do you know how much modern data there is for M. oralis?

Lena G (lena.granehall@gmail.com)
2020-09-21 15:51:13

*Thread Reply:* There's four modern genomes available

👍 James Fellows Yates, Kun Huang
Kun Huang (kun.huang@unitn.it)
2020-09-21 15:54:42

*Thread Reply:* As I know, there are only 4 modern RefSeqs of M. oralis, and maybe two modern calculus samples which contain well-covered M. oralis. These modern samples are all from @velsko or Mann et al. study.

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 15:56:19

*Thread Reply:* Thinking in terms of the variation graphs what would be good test data. Pathogen stuff obviously pretty good for that, but outside of that comes more difficult

👍 Kun Huang, Katerina Guschanski
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 15:50:38

as in comparative genomes?

Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-21 15:50:39

Has anyone else used the GreenGenes reference or RefSeq for their MapDamage analysis? I applied GreenGenes once before with dental calculus samples and was able to get damage plots.

Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-21 15:51:58

*Thread Reply:* But I wasn't very confident in the results.

Betsy Nelson (nelson@shh.mpg.de)
2020-09-21 16:05:06

*Thread Reply:* Hi Sterling...why not confident?

Maxime Borry (maxime.borry@gmail.com)
2020-09-21 16:14:17

*Thread Reply:* Very few reads mapped ?

Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-21 16:17:12

*Thread Reply:* There were about 10,000 reads that mapped but because those references are mixed with soil, oral, skin and all sorts of microbes, I wasn't sure how to interpret it. If I were to go back, I think it may make more sense to use the HOMD database as a reference for MapDamage. Has anyone tried this yet with dental calculus?

Polly
2020-09-21 16:03:28

@ivelsko has a poll for you!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:05:49

*Thread Reply:* @Lena G @Pooja Swali what do you use?

Pooja Swali (swalipooja@gmail.com)
2020-09-21 16:08:00

*Thread Reply:* htsbox majority consensus caller by Heng Li so far, but haven't done a careful evaluation

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:08:43

*Thread Reply:* Oooh, not heard of that. What is the possible advantagE?

Lena G (lena.granehall@gmail.com)
2020-09-21 16:12:55

*Thread Reply:* Angsd, but I've only used it for single genes so far.

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:03:51

@channel poll ☝️

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:12:15

I've also pinned the discussion points to the the channel! To see this, please press the 'i' button in the top right hand side of the chat (next to the display pictures)

👍 Lena G
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:15:18
ivelsko (velsko@shh.mpg.de)
2020-09-21 16:18:47

I think it’s worth considering the definition we use of strain. In the standard sense it suggests members of the same species that have different gene content. Here, it seems to mostly mean members of the same species with (enough) SNP differences. How does this affect the way we think about differentiating strains and the methods we use to do so?

Kun Huang (kun.huang@unitn.it)
2020-09-21 16:25:25

here is the very fresh & through review about strain lineation etc… https://pubmed.ncbi.nlm.nih.gov/32499497/

PubMed
👍 James Fellows Yates, Anna F.
Polly
2020-09-21 16:29:48

@ivelsko has a poll for you!

👀 Valentina Zaro
ivelsko (velsko@shh.mpg.de)
2020-09-21 16:31:49

multiVCFanalyzer

Polly
2020-09-21 16:33:09

@ivelsko has a poll for you!

Betsy Nelson (nelson@shh.mpg.de)
2020-09-21 16:35:05

What is the benefit to using freebayse over MultiVCF Analyzer?

Betsy Nelson (nelson@shh.mpg.de)
2020-09-21 16:35:14

ok I hear James

Lucy van Dorp (lucy.dorp.12@ucl.ac.uk)
2020-09-21 16:36:15

In case of use, this is a nice tool for reconstructing pan-genomes from a modern repertoire: https://www.biorxiv.org/content/10.1101/2020.09.11.293472v3.full

👍 Jaelle Brealey, aidanva
aidanva (aida.andrades@gmail.com)
2020-09-21 16:36:58

*Thread Reply:* I have a bit of experience with panX and also roary. Both easy to use but requires tweaking to incorporate ancient data

ivelsko (velsko@shh.mpg.de)
2020-09-21 16:37:28

*Thread Reply:* I found roary easy to use

Anna F. (annakfos@gmail.com)
2020-09-21 16:37:43

*Thread Reply:* PanACoTA is an excellent name

☝️ aidanva
🍨 James Fellows Yates
😍 Lucy van Dorp
Kun Huang (kun.huang@unitn.it)
2020-09-21 16:37:50

*Thread Reply:* agree, roary is very handy

Maxime Borry (maxime.borry@gmail.com)
2020-09-21 16:38:42

Anyone using DeepVariant ? https://github.com/google/deepvariant

Stars
<p>2070</p>
Language
<p>Python</p>
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 10:59:26

*Thread Reply:* ```DeepVariant supports:

Germline variant-calling in diploid organisms. For somatic data or any other samples where the genotypes go beyond two copies of DNA, DeepVariant will not work out of the box because the only genotypes supported are hom-alt, het, and hom-ref. The models included with DeepVariant are only trained on human data. For other organisms, see the blog post on non-human variant-calling for some possible pitfalls and how to handle them.``` sigh

Susanna Sabin (sjsabin@asu.edu)
2020-09-21 16:40:08

A nifty comparison of SNP calling pipelines for bacteria

👍 Lena G, aidanva
❤️ Betsy Nelson
Kelly Blevins (blevinske1@gmail.com)
2020-09-21 16:40:22

Here are potential alternatives to MultiVCFAnalyzer that I’ve been playing with: https://github.com/Integrative-Transcriptomics/MUSIAL https://github.com/tseemann/snippy https://github.com/sanger-pathogens/snp-sites

👍 Betsy Nelson
👍:skin_tone_4: Miriam Bravo
Kun Huang (kun.huang@unitn.it)
2020-09-21 16:41:28

*Thread Reply:* snp-sites works pretty well and extremely fast.

👍 Betsy Nelson, Kelly Blevins
Lucy van Dorp (lucy.dorp.12@ucl.ac.uk)
2020-09-21 16:41:30

*Thread Reply:* And this one too https://github.com/Amine-Namouchi/snpToolkit

Language
<p>Python</p>
Last updated
<p>a year ago</p>
👀 Kelly Blevins
Meriam Guellil (meriam.guellil.ac@gmail.com)
2020-09-21 16:41:55

*Thread Reply:* how have you found snippy with aDNA?

Kelly Blevins (blevinske1@gmail.com)
2020-09-21 16:46:21

*Thread Reply:* Haha I have only used snippy for making multi-sample SNP alignments because you must use their processing pipeline with little power to modify parameters. So I input bams that have been prepped using aDNA standards.

Meriam Guellil (meriam.guellil.ac@gmail.com)
2020-09-21 16:47:46

*Thread Reply:* yeah it is designed as a full pipeline so I was wondering how it does with aDNA bams and core snp alignments, but I guess we are back to lacking configuration options...

Jessica Hider (hiderj@mcmaster.ca)
2020-09-21 16:47:55

*Thread Reply:* A few of us in the poinar lab are using it like Kelly was saying

👍 Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:50:05

@channel has anyone tried more recent aligners? Like Minimap2/

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-21 16:53:49

Isn’t it a long read aligner?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:54:03

It's designed for but I'm pretty sure Heng said it has similar perofrmacne

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:54:05

to bwa

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:55:27

Has anyone had any experiences with aDNA specific genotypers: e.g. antCaller?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 16:55:36

https://github.com/BoyanZhou/AntCaller

Stars
<p>2</p>
Language
<p>Python</p>
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 17:23:25

Last call for questions for the entire session @channel!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 17:23:32

Also for people just listening in!

Kun Huang (kun.huang@unitn.it)
2020-09-21 17:24:05

Here is a tool to detect recombinant region: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004041

journals.plos.org
Kun Huang (kun.huang@unitn.it)
2020-09-21 17:25:22

detecting recombination from metagenome data : https://www.nature.com/articles/s41592-018-0293-7

Nature Methods
Nico Rascovan (nicorasco@gmail.com)
2020-09-21 17:31:23

Cool! Nice two ones

Kun Huang (kun.huang@unitn.it)
2020-09-21 17:32:33

ClonalFrameML works well when genome-alignment is small (30-50 taxa). The second one is pretty fast even for large-scale metagenomic datasets.

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-21 17:33:35

@channel does anyone of the workshop participants know MALT developers? Would like to have contacts to ask a few questions

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 17:34:51

*Thread Reply:* http://megan.informatik.uni-tuebingen.de/

megan.informatik.uni-tuebingen.de
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 17:34:56

*Thread Reply:* There is a dedicated section for MALT

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-21 17:37:01

*Thread Reply:* Ok, thanks @James Fellows Yates I think I tried that one, did not get answers on my questions, just wanted to see if somebody in the workshop is actually a MALT developer

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 18:10:16

*Thread Reply:* Ah no, they aren't present here.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 18:10:43

*Thread Reply:* But it's basically just Daniel who develops afaik

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-21 18:11:31

*Thread Reply:* Ok, thanks! Maybe I can throw my question to the community when touch MALT at this workshop?

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 18:17:39

*Thread Reply:* Go for it

Meriam Guellil (meriam.guellil.ac@gmail.com)
2020-09-21 17:33:50

gubbins is also widely used on bactieral data

Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-09-21 18:47:25

*Thread Reply:* I would just like to comment on how wonderful the name gubbins is.

😆 James Fellows Yates
👍 James Fellows Yates
Kun Huang (kun.huang@unitn.it)
2020-09-21 17:34:52

yes, agree that gubbins is also a nice one.

Kun Huang (kun.huang@unitn.it)
2020-09-21 17:36:36

But gubbins can only detect the recombinant stretch between taxa given. ClonalFrameML nonetheless can detect any recombination introduced. Just a bit computational-demanding with data growing.

Meriam Guellil (meriam.guellil.ac@gmail.com)
2020-09-21 17:38:12

I tend to use cfml, what I have observed with gubbins is that it has a tendency to output much smaller intervals, where cfml will cluster them and take into account non-core intervals

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 18:28:31

@channel starting in 2 minutes!

Jessica Hider (hiderj@mcmaster.ca)
2020-09-21 18:45:12

I'm using Refsoil as a database for soil contam (I don't have a soil sample from this site 😞 ) and was curious what others are using database-wise

Anna F. (annakfos@gmail.com)
2020-09-21 18:48:37

I would also like to know what people with “unconventional” data sets (ie not human calculus) that do not have good reference databases to compare against in Source Tracker or your favourite tool?

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 18:53:40

we have developed a workflow that exploits the MGnify API to generate training sets for mt-ST. It uses the MGnify biome information to query data from MGnify. Now we are implementing the training of mt-ST for ancient samples

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 18:54:33

check slide 3 from here, we are going to make it public soon

👍 Susanna Sabin
🙂 Jessica Hider
Vilma Perez (vilma.perez@adelaide.edu.au)
2020-09-21 19:13:56

My samples come from extreme environments and specially for thermophilic or acidophilic species I don't see any DNA damage. Of course I wouldn't do any big assumptions right now because I am still working on that. Also there a lack of reference genomes for this type of species

Vilma Perez (vilma.perez@adelaide.edu.au)
2020-09-21 19:14:32

but is definitely something to look into

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 19:15:01
Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-21 19:15:03

We have also some palaeofaeces samples from very arid environments and see almost no damage either despite the samples being dated to 1300 BP.

Lena G (lena.granehall@gmail.com)
2020-09-21 19:15:28

*Thread Reply:* same!

Vilma Perez (vilma.perez@adelaide.edu.au)
2020-09-21 19:17:17

*Thread Reply:* yes!

Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-21 19:15:28

So water is necessary to accumulate aDNA damage patterns.

Nico Rascovan (nicorasco@gmail.com)
2020-09-21 19:25:18

It makes totally sense. Definitely the lack of aDNA degradation patterns in microbial data is highly frequent. It would be something to quantify somehow. I think for the field is something that will help many, to have an article to reference to when degradation patterns are not seen in our datasets.

👍 Åshild (Ash), Lena G, Jessica Hider, Katerina Guschanski
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:28:46

we are exploring ways to circumvent this problem by exploiting the differences of codon usage of the sequences in our samples

Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-21 19:29:22

*Thread Reply:* You mean regarding the lack of aDNA patterns?

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:29:30

*Thread Reply:* yes

Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-21 19:29:31

*Thread Reply:* OK, thanks!

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:30:54

*Thread Reply:* it might not be a universal solution but for certain situations might be useful. The stuff we are doing is inspired by this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799439/

PubMed Central (PMC)
Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-21 19:32:14

*Thread Reply:* The only problem I could see is how to persuade the reviewer that is a non-standard, but valid approach. 😉

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:33:36

*Thread Reply:* microbes and their special needs 🙂

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:35:38

*Thread Reply:* there is a lot of info hidden in the coding space that we can exploit in combination with the methods of @Nikolay Oskolkov

Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-21 19:36:35

*Thread Reply:* Definitely, there is a lot of reference data to train for codon usage.

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:43:34

*Thread Reply:* when we don’t have references, we use a super-read like approach to partition potential ancient reads

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:44:25

*Thread Reply:* This is in one of the slides for tomorrow’s talk

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:45:05
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-21 19:29:22

there are certain signatures that might be useful when there is no damage

Polly
2020-09-21 19:29:33

@Maxime Borry has a poll for you!

Polly
2020-09-21 19:29:48

@ivelsko has a poll for you!

Nico Rascovan (nicorasco@gmail.com)
2020-09-21 19:34:21
👍:skin_tone_2: Anna F.
👍 Ele, Sterling Wright
Pooja Swali (swalipooja@gmail.com)
2020-09-21 19:46:14

We also use this as an alternative to Mapdamage but is mainly useful for samples that are UDG treated https://github.com/pontussk/PMDtools

Stars
<p>3</p>
Language
<p>Python</p>
👍:skin_tone_3: Anna F., Åshild (Ash)
Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-21 19:48:22

@James Fellows Yates James, are you suggesting that we need something like the standard PCA plot standard for the pop gen folks?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 19:48:50

*Thread Reply:* Will ask next!

Anna F. (annakfos@gmail.com)
2020-09-21 19:59:26

We all look terrified now.

😱 James Fellows Yates
😂 Ele, Jonas Niemann
Maxime Borry (maxime.borry@gmail.com)
2020-09-21 20:00:45

I would say you can compare but need to record the metadata, and do some statistical modelling taking them into account. Combat and Songbird are nice tool for that https://github.com/biocore/songbird https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2263-6

Stars
<p>29</p>
Language
<p>Python</p>
Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-21 20:01:18

I agree, it is time to introduce generalized linear models into microbiome analysis.

👍 Betsy Nelson, Emrah Kırdök, Nico Rascovan, Jaelle Brealey
:mask_parrot: Anna F.
Vilma Perez (vilma.perez@adelaide.edu.au)
2020-09-21 20:01:45

yeap that;s something that is going to be very useful!

Maxime Borry (maxime.borry@gmail.com)
2020-09-21 20:07:03

https://evayiwenwang.github.io/Managing_batch_effects/

evayiwenwang.github.io
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-21 20:08:04

@Maxime Borry and @Alex Hübner all batch-effects correction tools will work providing that the signal is orthogonal to the batch. With 100% confounding when reference and query samples were sequenced using different platforms I would not put them on the same PCA plot :)

Maxime Borry (maxime.borry@gmail.com)
2020-09-21 20:13:09

*Thread Reply:* Agree, can’t compare 16s and WGS data for example, or metagenomic profiles generated by classifying agains different databases, or different tools. As an optimistic note: keeping track of the metadata and visualising their effect, on let’s say a PCA colored by batch effect, will give a good starting indication of whether or not this is something to worry about

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-21 20:45:32

*Thread Reply:* True! I usually make a correlation heatmap of my PCs against all available meta-data to understand the sources of variation in my data. If my PC1 is mostly explained by the batch variable, it is very worrying

Maxime Borry (maxime.borry@gmail.com)
2020-09-21 20:09:20

Last one on batch effect correction for tonight: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1850-9

Genome Biology
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 10:21:00

@channel I've just made a channel for people working on ancient microbial genomics (e.g. single genomes of pathogens, commensals etc). <#C01B511KU91|microbial-genomics> . Please join if you work in this area!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 13:06:35

Code of conduct: https://spaam-community.github.io/#/spaam2/codeofconduct

spaam-community.github.io
Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 13:20:20

Even though a side effect of unethical practices is data which is not publicly available, I think it should be considered that many Indigenous groups do not want their data to be public.

👍 Freddi Scheib, aidanva, Jessica Hider, Åshild (Ash), Anna F.
Marcel Keller (marcel.keller@ut.ee)
2020-09-22 13:23:01

*Thread Reply:* But is it in this case ethical to work on that at all?

Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 13:23:33

*Thread Reply:* I think it depends on the group.

Christina Warinner (warinner@shh.mpg.de)
2020-09-22 13:53:45

*Thread Reply:* What is the motivation behind making the data not public?

Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 13:23:03

Both the side effects and by extension the solutions are not one size fits all in this case BUT I think as Miriam said it will take increased interaction and involvement with existing descendent communities for Indigenous communities to practice ethically.

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 13:25:16

the data will depend if it is under the Fort Lauderdale Agreement, in addition if the country is under Nagoya

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 13:25:41

Fort Lauderdale Agreement: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672783/

PubMed Central (PMC)
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 13:26:06

of course this is for genomic data, no idea about other types of data

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 13:26:23

one gets lost with all this stuff

Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 13:26:28

Yes but I would argue that these and also NAGPRA fall short so we have to take a bit more responsibility in this.

Anna F. (annakfos@gmail.com)
2020-09-22 13:26:57

there is also a time limit - ie when samples were collected , if they are in museums abroad for decades before being sampled etc

Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-22 13:27:42

*Thread Reply:* Especially museum samples collected along time ago, e.g. during colonial times are a delicate issue.

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 13:27:07

I guess there are the needs of aligning all sites involved

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 13:27:30

Questions for voting for Nico - Put emoji reactons to those you are most interested in!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 13:27:36

"Data clean-up: How far can we go?"

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 13:28:06

I guess having a DIR of institutions (legal, ethical…) would be also very useful

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 13:28:18

"Taxonomic levels: What’s the right size for the lens?"

Polly
2020-09-22 13:29:20

@James Fellows Yates has a poll for you!

Polly
2020-09-22 13:30:52

@James Fellows Yates has a poll for you!

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 13:46:03
Nico Rascovan (nicorasco@gmail.com)
2020-09-22 13:46:35

that's also to discuss 👆

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 13:48:12

And I copy here the other slides in case it helps refreshing the sub-items of each point in the poll

Freddi Scheib (freddischeib@gmail.com)
2020-09-22 13:48:36

A note on radiocarbon reporting conventions

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2020-09-22 13:53:26
Nico Rascovan (nicorasco@gmail.com)
2020-09-22 13:54:57

Regarding SOPs, these are some items we wrote with James: Benchmarking: What analyses should everyone do? (e.g., compare to source-tracker) What validation tests should be run? What data should be used? Which datasets for training (e.g., for machine learning)

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 13:57:16

maybe we should have our own branch of CAMI: https://data.cami-challenge.org/ maybe we should contact them

ivelsko (velsko@shh.mpg.de)
2020-09-22 14:00:55

*Thread Reply:* @Maxime Borry has spoken with the person leading this but found she wasn’t very interested. Maybe having a group collectiveley approach would be more persuasive

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:02:00

*Thread Reply:* Yes, I can get in touch through the people from my former group in Bremen, when CAMI appeared they contacted us

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:02:41

*Thread Reply:* at that time was Alexander Sczyrba

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:05:10

*Thread Reply:* Well, let’s say that no one went forward with it.

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:06:02

*Thread Reply:* There is also the LEMMI benchmarking challenge that is quite interesting, because it is updated in real time https://lemmi.ezlab.org/#/ We contacted them, but it also didn’t go forward https://gitlab.com/ezlab/lemmi/-/issues/5

GitLab
Author
Maxime Borry
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:09:07

*Thread Reply:* This should be coupled with the lab standards @Christian Carøe was talking about. For example the guys from the XMP develop this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345951/ In last year GSC meeting Scott presented their standards

PubMed Central (PMC)
ivelsko (velsko@shh.mpg.de)
2020-09-22 13:57:49

This is the paper Jamesis referring to: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003531

journals.plos.org
👍 Anneke ter Schure, James Fellows Yates
Jessica Hider (hiderj@mcmaster.ca)
2020-09-22 14:03:19

*Thread Reply:* great paper! I had the same issue James (i.e. how to norm? etc.)

ivelsko (velsko@shh.mpg.de)
2020-09-22 13:58:20

And this one: https://www.frontiersin.org/articles/10.3389/fmicb.2017.02224/full

Frontiers
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 13:58:45

👍

Polly
2020-09-22 14:09:58

@James Fellows Yates has a poll for you!

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:10:18

Speaking as a PI here: Testing is super important, but I'd want my people to come out of my lab with a portfolio that would allow them to pursue whatever career they want. If it is a career in science, they will need publications. Testing will not result in a pub...

👍:skin_tone_3: Anna F., Kun Huang
👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:11:30

*Thread Reply:* But then who should do the testing? I would disagree testing doesn't result in a publication..., 50% of bioinformatics is just hat 😆

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:12:48

*Thread Reply:* Bioinformaticians with permanent positions, e.g. as those offered by SciLifeLab

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:13:08

*Thread Reply:* Permanent positions?! They are a thing!?!?! 😉

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:13:42

*Thread Reply:* Positions in core-facilities are not necessarily permanent 😉

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:14:12

*Thread Reply:* Those at SciLifeLab are 🙂

😱 James Fellows Yates
Jaelle Brealey (jaelle.brealey@ntnu.no)
2020-09-22 14:14:20

*Thread Reply:* I was also referring to what I myself have an interest in - it's not so much whether I will get a publication out of it, it's also what I'm interesting in doing, which is more data analysis, not testing. But I agree testing is super important and useful!

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 14:18:51

*Thread Reply:* I think that testing is good and necessary, but it is necessary to put an end at some point, choose one solution we believe that will satisfy reviewers and community, and focus on the questions of the project. I personally care much more about questions than methods. So as long as the method is sounding, although not perfect, I prefer to move on

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:32:22

*Thread Reply:* I also find it interesting (@Katerina Guschanski), although you say testing will not result in pub, there is clearly a need for these testing papers as it seems one of the biggest concerns of people (particularly from the session yesterday). So if someone was to do that, and publish it, in principle they could get lots of citations?

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:34:49

*Thread Reply:* Absolutely true and a super good point. I/we would be happy to be able to use such guidelines. Also perfect arguments to provide to reviewers when they go "Why didn't you use this or that tool...?". So I guess the truth is somewhere in the middle. Periodic testing of new tools to compare to winners from the previous round?

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:43:36

*Thread Reply:* Exactly, if we had a CAMI-like dataset, so a 'gold standard' for people to test - would you feel more comfrotable for a student to spend time on it?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:44:19

*Thread Reply:* In the sense there is already a precedence

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:45:24

*Thread Reply:* for this we need a way to generate ancient mock communities in the lab, no idea if this is a thing

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:46:11

*Thread Reply:* Nope, I don't think we could do that; unless we get a single Mammoth femur and freeze it

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:47:04

*Thread Reply:* But we would need stuff for different contexts; this isn't just microbes

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:47:24

*Thread Reply:* one step at a time

😉 James Fellows Yates
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:47:32

*Thread Reply:* That would be perfect (using a mock community for tool testing periodically). Ideally coordinated effort across labs with multiple participating researchers.

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:49:05

*Thread Reply:* Wouldn't it be possible to produce a "simulated" community with typical aDNA traits: Damage, contamination, fragmentation patterns, etc. It is possible for hosts...

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:49:48

*Thread Reply:* Yeah I guess. IIRC CAMI had both synthetic dataset and also a 'real' mock community (with spiked in stuff)

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:50:01

*Thread Reply:* yep the real stuff is the interesting

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:50:14

*Thread Reply:* Exactly, we can't really model aDNA datasets very well atm

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:50:16

*Thread Reply:* the synthetic should not be a problem

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:50:45

*Thread Reply:* Well, we don't know the ground truth of a real aDNA dataset at the moment 🙂

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:51:25

*Thread Reply:* Yeah like Gargammel uses a Neanderthal damage profile... because everyone is analysing that...

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:52:23

*Thread Reply:* you, can use your sample patterns, but I think we need more realistic models

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:53:19

*Thread Reply:* @Nikolay Oskolkov I guess we could use some DL to generate more reliable syntcomms

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:53:28

*Thread Reply:* You mean even more complicated than what we currently think is already nightmare 🙂?

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:53:51

*Thread Reply:* yes

ivelsko (velsko@shh.mpg.de)
2020-09-22 14:10:55

I disagree. Publications are only necessary if one goes into academia

ivelsko (velsko@shh.mpg.de)
2020-09-22 14:11:27

This kind of testing would be great for someone who wants to go into industry, especially in bioinformatics work which is in high demand

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:12:13

Agree with @ivelsko. That's why I said career in science (meaning academia, sorry, should have been more precise).

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:20:11

For those in Germany you have https://www.gfbio.org/ for this

gfbio.org
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:28:03

and the standard: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511511/

PubMed Central (PMC)
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:34:24

https://researchparasite.com/

😆 James Fellows Yates
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 14:35:53
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:38:37

Notorious C.P.H

😆 Pete Heintzman
Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 14:42:05

Yes for some funding bodies and journals requiring data upload

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:44:30

*Thread Reply:* > Examples of activities that alone (without other contributions) do not qualify a contributor for authorship are acquisition of funding; general supervision of a research group or general administrative support; and writing assistance, technical editing, language editing, and proofreading. Those whose contributions do not justify authorship may be acknowledged individually or together as a group under a single heading (e.g. “Clinical Investigators” or “Participating Investigators”), and their contributions should be specified (e.g., “served as scientific advisors,” “critically reviewed the study proposal,” “collected data,” “provided and cared for study patients”, “participated in writing or technical editing of the manuscript”).

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 14:44:43

As far as I know, there are no structures in place to enforce or penalise authors/researchers who do not make data publicly available. Neither from journals nor from funders. These are general requirements, but even if journals are alerted to the violation of this rule, they cannot do anything about it (or at least don't do anything).

🤦 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 14:44:45

Also the CREDIT one: https://casrai.org/credit/

CASRAI
Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:48:11
Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:48:32

*Thread Reply:* > Acquisition of funding, collection of data, or general supervision of the research group alone does not constitute authorship.

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:52:24

Most modern microbiome samples do not include human DNA

ivelsko (velsko@shh.mpg.de)
2020-09-22 14:52:49

*Thread Reply:* How did you estimate this? I disagree from my experience with them

ivelsko (velsko@shh.mpg.de)
2020-09-22 14:53:07

*Thread Reply:* I think SRA may screen and mask the human reads

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 14:53:11

*Thread Reply:* Stripped before uploading to ENA

Polly
2020-09-22 15:01:27

@James Fellows Yates has a poll for you!

Polly
2020-09-22 15:02:46

@Maxime Borry has a poll for you!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 15:03:02

*Thread Reply:* \don't know 😆

☝️ aidanva, Katerina Guschanski
👍 Jessica Hider
ivelsko (velsko@shh.mpg.de)
2020-09-22 15:03:15

In some cases it is withheld for ethical reasons

ivelsko (velsko@shh.mpg.de)
2020-09-22 15:04:37

*Thread Reply:* Some large biomedical studies

Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-22 15:09:32

*Thread Reply:* Or you have to apply to some ethical body that sometimes they come back to you and sometimes not. E.g. dbGAP.

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 15:19:32

protocols.io ?

❤️ James Fellows Yates, Zandra Fagernäs
👍 Meriam Guellil, Åshild (Ash)
Anna F. (annakfos@gmail.com)
2020-09-22 15:27:29

Most common question I used to get from curators : “Why should i give you the sample and not wait for the next technological revolution in 10,15,20 years?”

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 15:28:24

*Thread Reply:* Second that!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 15:29:10

*Thread Reply:* Because we can 'immortalise' libraries 😉 (according to the mantra of a certain JK)

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 15:29:38

*Thread Reply:* Hahaha! I admit to have used this argument in the early years...

Anna F. (annakfos@gmail.com)
2020-09-22 15:29:50

*Thread Reply:* but if the data cannot be compared to anything else (from our conversation yesterday) is it really a bioarchiving of samples?

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 15:29:57

*Thread Reply:* It did come from the same source

Polly
2020-09-22 15:28:43

@James Fellows Yates has a poll for you!

Ele (eg715@york.ac.uk)
2020-09-22 16:28:46

*Thread Reply:* This is really interesting - thanks for asking!

Polly
2020-09-22 15:29:45

@James Fellows Yates has a poll for you!

Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 15:29:50

I think it's also important to remember that many archaeologists are working from an export permit where they specified research agendas that may not be in line with all the results metagenomic approaches can lead to.

Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 15:30:45

For example working with pathogens.... if our archaeologist specified TB in a research proposal and export permit but we found something else, we cannot reconstruct that and work with that.

Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 15:30:50

In some cases

👍 Maxime Borry, Sterling Wright, Clio Der Sarkissian, Åshild (Ash)
Nico Rascovan (nicorasco@gmail.com)
2020-09-22 15:53:08

share the group photo James

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 15:53:16

😁

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 15:53:17

I have to make notes

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 15:53:36

I've shared it with the other organisres, someone else will clear it up 😉

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 16:00:02

@channel if there is anyone not comfortable sharing their picture in the group photo on twitter, please let one of the organisers know

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 16:00:11

If anyone missed the group photo, please let me know

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 16:00:31

And we will take single-ones later and do some photoshop magic

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-22 16:02:50

Assembly+binning is a standard analysis in modern metagenomics. We are hesitant to do it in ancient metagenomics because assembly is a very complex step that needs lots of reads, do we even have enough coverage in ancient microbiome?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 16:03:10

*Thread Reply:* Depends on the sample; bigger problem is short read lengths

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:03:30

*Thread Reply:* not always, there are other alternatives than MAGs

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 16:04:01

*Thread Reply:* It worked well for us for some (highly abundant) species from historical dental calculus samples

👍 James Fellows Yates, Jaelle Brealey, Anna F.
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:04:37

*Thread Reply:* i work with very complicated samples, and is very challenging

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:04:48

*Thread Reply:* so the traditional approach doesn’t work

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:05:18

*Thread Reply:* this is like going back 10 years back in time in metagenomics

Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2020-09-22 16:05:53

*Thread Reply:* How do you handle the aDNA damages during the the assembly?

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:06:24

*Thread Reply:* we are working on integrating this in the assembly process

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:06:32

*Thread Reply:* I will show briefly

👍 Mohamed Sarhan
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:06:46

*Thread Reply:* also not using de brujin approaches

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 16:03:30

there are some papers where they did de novo assembly of microbial genomes

Anna F. (annakfos@gmail.com)
2020-09-22 16:05:14

*Thread Reply:* very true but it was targeted - not an open exploration. There are only a handful of papers fidning ancient MAGs

Anna F. (annakfos@gmail.com)
2020-09-22 16:12:11

*Thread Reply:* One of the few recovering ancient MAGs by @Katerina Guschanski and @Jaelle Brealey https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa135/5848415

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 16:14:32

*Thread Reply:* The limitation is: these are very recent samples my most standards (within the last century) and the used approach worked for highly abundant species

Anna F. (annakfos@gmail.com)
2020-09-22 16:15:13

*Thread Reply:* Exactly! Hence the need for the combination of assembly plus assembly free methods

Anna F. (annakfos@gmail.com)
2020-09-22 16:15:21

*Thread Reply:* but it opens very exciting possibilities

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-22 16:15:35

*Thread Reply:* Agreed 🙂

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 16:03:48

The one on dental calculus from C. Warinner is an example

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-22 16:10:02

Ok, I understand that doing assembly+binning you will discover new unknown microbes. How would you interpret and analyze those microbes?

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:10:46

*Thread Reply:* for example http://merenlab.org/2016/11/08/pangenomics-v2/

Meren Lab
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:11:07

*Thread Reply:* we have a full workshop every year on this

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:11:28
Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-22 16:11:48

*Thread Reply:* For Maxime and me, we mainly work on very well described datasets, like human gut or human oral microbiome, which makes it easier to compare to known data. For unknown environments, it is more complicated.

Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-22 16:18:43

*Thread Reply:* @Antonio Fernandez-Guerra Is it too late to sign up for the workshop for this year?

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-22 16:19:43

*Thread Reply:* I would also be interested in attending this workshop

Anna F. (annakfos@gmail.com)
2020-09-22 16:21:26

*Thread Reply:* it is an excellent workshop! But sadly i dont think it is happening this year.

Anna F. (annakfos@gmail.com)
2020-09-22 16:21:52

*Thread Reply:* however keep your eyes on twitter or email Louis for further info for when they host it next: lois.maignien@univ-brest.fr

Anna F. (annakfos@gmail.com)
2020-09-22 16:22:22

*Thread Reply:* Also bear in mind this is not geared for ancient metagenomes

Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-22 16:23:06

*Thread Reply:* Thank you @Anna F.!

Anna F. (annakfos@gmail.com)
2020-09-22 16:24:17

*Thread Reply:* there will be some online courses available early next year if that would be interesting? again not necessarily ancient

Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-22 16:25:56

*Thread Reply:* I would still be itnerested. Are they hosted by the same people?

Anna F. (annakfos@gmail.com)
2020-09-22 16:26:24

*Thread Reply:* partially! Tom Delmont will be on the teachers. It will be a short course so an intro to the field

👍 Sterling Wright
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:36:04

*Thread Reply:* Next year unfortunately

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:38:10

*Thread Reply:* @Nikolay Oskolkov this one https://www.biorxiv.org/content/10.1101/490078v2 from Simon Rasmussen is using Variational Autoencoders

👍 Nikolay Oskolkov
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:38:14

*Thread Reply:* to bin MAGs

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:39:10

*Thread Reply:* CONCOCT from Chris Quince https://pubmed.ncbi.nlm.nih.gov/25218180/ works very nicely

PubMed
👍 Nikolay Oskolkov
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:40:39

*Thread Reply:* this last one from Chris is also super cool https://www.biorxiv.org/content/10.1101/2020.09.06.284828v1.full

bioRxiv
Polly
2020-09-22 16:25:45

@Anna F. has a poll for you!

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:41:34

@Maria Spyrou https://pubmed.ncbi.nlm.nih.gov/31235882/ PLASS

PubMed
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:42:29

PenguiN: https://twitter.com/thesteinegger/status/1306245987048910849

twitter
} Martin Steinegger (마틴 스타이네거) (https://twitter.com/thesteinegger/status/1306245987048910849)
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:42:52

now we are trying to model damage during the assembly process

Maria Spyrou (spyrou@shh.mpg.de)
2020-09-22 16:43:15

Thank you!

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 16:44:05

we have ways to cluster co-abundant genes that might come from the same population

Polly
2020-09-22 16:46:07

@ivelsko has a poll for you!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 16:47:47

@channel poll!!!! ☝️

Lena G (lena.granehall@gmail.com)
2020-09-22 17:06:50

@Nikolay Oskolkov what kind of artefacts did you get for those early assemblies? How did they not work?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:13:51

@Nico Rascovan @Antonio Fernandez-Guerra what would you like your channel to be called?

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 22:58:30

*Thread Reply:* What do you mean? Any channel, or something related to what we discussed today with the assembly of aDNA data? Antonio knows about it, I am just interested on it, but I'm still very ignorant on this respect

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-23 09:15:28

*Thread Reply:* I would add one like New computational methods or something similar, where we can discuss new approaches

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 09:18:40

*Thread Reply:* analysis-hipsters? ;)

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-23 09:20:35

*Thread Reply:* also one channel with something like Matchmaking for potential new collaborations

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 11:45:26

*Thread Reply:* You guys should be able to make these channels actually 🤔. Make them and advertise on #general! If you can't let me know

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 17:16:24

about unknowns… (shameless self promotion) http://merenlab.org/2020/07/01/dark-side/

Meren Lab
ivelsko (velsko@shh.mpg.de)
2020-09-22 17:23:43

The papers that describe the assembly methods used by the Segata lab are: https://www.sciencedirect.com/science/article/pii/S0092867419300017?via%3Dihub

sciencedirect.com
ivelsko (velsko@shh.mpg.de)
2020-09-22 17:23:54

https://www.sciencedirect.com/science/article/pii/S1931312819304275?via%3Dihub

sciencedirect.com
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:24:29

With P. copri has ancient genomes

Kun Huang (kun.huang@unitn.it)
2020-09-22 17:26:42

*Thread Reply:* Yes, but very fragmented. ~40% region is confidently covered.

👍 James Fellows Yates
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 17:25:46

http://merenlab.org/2016/12/14/coverage-variation/

Meren Lab
🏄‍♂️ James Fellows Yates
Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2020-09-22 17:43:54

Has anyone compared assemblies of UDG-treated and non-treated samples?

👍 Jonas Niemann
Åshild (Ash) (ashild.v@gmail.com)
2020-09-22 17:44:38

Good question

aidanva (aida.andrades@gmail.com)
2020-09-22 17:45:02

I have only worked with UDG-treated samples

aidanva (aida.andrades@gmail.com)
2020-09-22 17:45:25

but it will be interesting to actually see the comparison

ivelsko (velsko@shh.mpg.de)
2020-09-22 17:45:26

@Maxime Borry showed that the damage doesn’t make a difference, only the read length does

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 17:45:52

*Thread Reply:* **much of a difference

Alex Hübner (alexander_huebner@eva.mpg.de)
2020-09-22 17:45:51

But we didn’t simulate UDG-treated data, only non-treated.

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 17:46:59
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:48:08

@channel please post in the thread to this message any papers you know they performed assemblies of aDNA data!

Lena G (lena.granehall@gmail.com)
2020-09-22 17:50:26

*Thread Reply:* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5643016/ Luhmann 2017

PubMed Central (PMC)
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:50:57
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:51:05
Lena G (lena.granehall@gmail.com)
2020-09-22 17:51:58

*Thread Reply:* hep B: https://elifesciences.org/articles/36666

eLife
Mike Martin (sameoldmike@gmail.com)
2020-09-22 18:31:29

*Thread Reply:* https://www.nature.com/articles/ncomms3172

Nature Communications
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:48:20

And we can make a bioliography

❤️ Betsy Nelson
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:49:18
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:49:52
aidanva (aida.andrades@gmail.com)
2020-09-22 17:51:19

*Thread Reply:* assembly for y. pestis: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5643016/

PubMed Central (PMC)
Åshild (Ash) (ashild.v@gmail.com)
2020-09-22 17:55:49

*Thread Reply:* Assembly for ancient S. enterica Paratyphi C https://www.cell.com/current-biology/pdfExtended/S0960-9822(18)30694-8

Pete Heintzman (peteheintzman@gmail.com)
2020-09-22 18:24:45

*Thread Reply:* A couple from the lake sedaDNA world: https://www.biorxiv.org/content/10.1101/2020.04.10.035535v1 https://www.biorxiv.org/content/10.1101/2020.01.06.896068v1

bioRxiv
bioRxiv
Kun Huang (kun.huang@unitn.it)
2020-09-22 17:48:41

As I know, there are very few. I know a very bad one

🤫 James Fellows Yates
Kun Huang (kun.huang@unitn.it)
2020-09-22 17:49:02

I will find and post it here later

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:50:39

THREAD!

aidanva (aida.andrades@gmail.com)
2020-09-22 17:51:03

*Thread Reply:* sorry!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:51:21

*Thread Reply:* 😅 sorry I panicked as people were posting on different ones

🤣 Betsy Nelson
Lena G (lena.granehall@gmail.com)
2020-09-22 17:53:33

*Thread Reply:* now there are several threads...

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:57:00

*Thread Reply:* 🤦 James fail

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:57:08

*Thread Reply:* I'll collcet them all in one place 😅

👍 Lena G
Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2020-09-22 17:50:52

Thanks !

Nico Rascovan (nicorasco@gmail.com)
2020-09-22 17:54:56

Hey all, I am 100% positive about any intiative to continue and develop further the SPAAM community. I won't be able to attend at 19h, because I am taking care of my daughters now. It was a great e-meeting and I am very happy to have seen you all. See you all soon, I hope!

👍 Kun Huang, Sterling Wright, Pete Heintzman, Maria Spyrou, Katerina Guschanski
🙂 Jessica Hider
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-22 17:55:26

*Thread Reply:* same here!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 17:56:39

*Thread Reply:* Feel free to post (if you have time) specifci things you would like to have/see

Linda Armbrecht (linda.armbrecht@utas.edu.au)
2020-09-22 18:36:30

*Thread Reply:* Hey, same for me here, I wont be able to make it to the last session. Thanks so much for organising and it was nice meeting you, also very interested to continue the communication in the future - I really like the idea of little workshops, maybe on assemblies :)

👍 James Fellows Yates
Jessica Hider (hiderj@mcmaster.ca)
2020-09-22 18:01:18

Just as a note, I'm new to assembly but, I tried denovo for a single genome with min30 vs min45 bp using SPAdes and found that min45 performed slightly better (assessed with QUAST and BLASTing post assembly). Min35 had more 'non-target' DNA (though I didn't filter out human, nice point on that today).

👍:skin_tone_3: Anna F.
Anna F. (annakfos@gmail.com)
2020-09-22 18:11:32

*Thread Reply:* Good to know! i’ve seen both to be honest - filtering out the host and not filtering out the host- it really seems to depend whose modern metagenomic papers you come across!

👍 Jessica Hider
Jessica Hider (hiderj@mcmaster.ca)
2020-09-23 23:45:33

*Thread Reply:* Thanks for saying that!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 18:29:30

@channel remember everyone can unmute themselves and contribute in the final session 😄

👍 Emrah Kırdök
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-22 19:00:05

@channel we are about to start, webcams on please! Listeners as well!

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 19:22:54

The LEMMI benchmark

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 19:22:58
Lucy van Dorp (lucy.dorp.12@ucl.ac.uk)
2020-09-22 19:27:42

Here is a link to a 'metagenomics reporting guidelines' paper just out, so there is precedent for this type of paper for modern datasets. Something similar could work for aDNA and I would think would be widely cited https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30199-7/fulltext

Maxime Borry (maxime.borry@gmail.com)
2020-09-22 19:28:13

The workshop on reproducibility that we hosted at the Max Planck in Jena last year: https://rrdm-shh.github.io

rrdm-shh.github.io
Lucy van Dorp (lucy.dorp.12@ucl.ac.uk)
2020-09-22 19:35:49

Just another example I mentioned https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000335

microbiologyresearch.org
👍 Åshild (Ash)
Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-09-22 19:52:56

Got to go, but thanks very much everyone! Looking forward to digesting all of this.

👍 Maxime Borry
:mask_parrot: James Fellows Yates
😀 Jessica Hider
Shreya (shreya23@uchicago.edu)
2020-09-22 19:59:02

Likewise-- thank you all! Excited for everything to come!

👍 Maxime Borry
:mask_parrot: James Fellows Yates
😀 Jessica Hider
Betsy Nelson (nelson@shh.mpg.de)
2020-09-22 19:59:45

Thank you so much everyone!! This was GREAT! 😁

👍 Maxime Borry
:mask_parrot: James Fellows Yates
😀 Jessica Hider
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-22 20:00:35

Really enjoyed the workshop, the organizers have done an outstanding job, thanks a lot everyone!

👍 Betsy Nelson, Maxime Borry
:mask_parrot: James Fellows Yates
😀 Jessica Hider
aidanva (aida.andrades@gmail.com)
2020-09-22 20:00:45

Thank you everyone!!

👍 Betsy Nelson, Maxime Borry
:mask_parrot: James Fellows Yates
😀 Jessica Hider
Maria Spyrou (spyrou@shh.mpg.de)
2020-09-22 20:01:29

Thanks all so much for this, especially the organisers for putting this together! Hope to see everyone in person soon!

👍 Betsy Nelson, Maxime Borry
:mask_parrot: James Fellows Yates
😀 Jessica Hider
Ele (eg715@york.ac.uk)
2020-09-22 20:02:11

Thank you to everyone for interesting talks and discussion and especially the organisers of course! Very reassuring to hear others often feel alone - but look at us all! 💪

👍 Betsy Nelson, Maxime Borry
:mask_parrot: James Fellows Yates
😀 Jessica Hider
Sterling Wright (sterlingwright2016@utexas.edu)
2020-09-22 20:02:15

Thank you everyone! This was a terrific experience. Big congratulations to the organizers who pulled this off! All y’all are improving the field as a whole

👍 Betsy Nelson, Kelly Blevins, Maxime Borry, Becky Cribdon
:mask_parrot: James Fellows Yates
😀 Jessica Hider
Emrah Kırdök (emrahkirdok@gmail.com)
2020-09-22 20:09:26

Thank you everyone for this great meeting!

:mask_parrot: James Fellows Yates
😀 Jessica Hider
Lucy van Dorp (lucy.dorp.12@ucl.ac.uk)
2020-09-22 20:21:49

Thanks for hosting a great event, apologies I couldn't attend for more. I got a lot out of it and am excited to see what comes out of the community and discussions 😁

:mask_parrot: James Fellows Yates
😀 Jessica Hider
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 08:23:07

@channel we will keep this channel open for a few more months until notes are shared etc, but in the meantime Irina and I have created the different channels for all the working groups that people said they would be interested in talking in (and add those who put their names on the google sheet):

Working group on standardising metadata <#C01BX7EM4EL|metadata-standards> CAMI challenge-like benchmarking datasets/challenge <#C01BDHQP3EY|benchmark-datasets> Standardising authentication criteria <#C01B7J8M2JX|authentication-standards> Open letter on data sharing #datasharing Workshop on data reproducibility (conda, docker, github etc. etc.) <#C01B7CA42AE|analysis-reproducibility> Lab comparison: Broad lab extraction/library building testing w/ the same sample <#C01BJPKHH9P|lab-community> Cross-lab pipeline testing (e.g. genome reconstruction, or taxonomic profiles) <#C01B49RM353|analysis-comparison-challenge> SPAAM3 <#C01BL1HD57T|spaam3-organisers>

Remember these are open, you can join/leave when you want. And it is up to the people in each channel to decide how to run things! We look forward to seeing what comes out of these 🙂.

👍 Sterling Wright
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 08:25:24

And finally, some general discussion channels:

Ancient microbiomes <#C01BDJBM1PE|ancient-microbiomes> Ancient microbial genomics (e.g. pathogens) <#C01B0LND80N|ancient-microbial-genomics> seda/environmental DNA <#C01B7CRJK7U|seda-dna>

Anna F. (annakfos@gmail.com)
2020-09-23 09:27:55

and to add: De novo assembly and genome resolved metagenomics (e.g the unknown fraction of ancient metagenomes and what was covered in session 5) <#C01B7FPCBKL|de-novo-assembly>

👍 Kun Huang, Katerina Guschanski
😀 Jessica Hider
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-23 17:40:10

Hi guys, do not know what channel to address this question to, so posting it here. Does anyone have a way to work with the SAM-alignments produced by MALT aligner? There is a known issue with CIGAR string for a number of alignments that MALT generates, that makes the SAM-file produced by MALT impossible to be processed using samtools. I can use bash/awk or python for manual processing the MALT alignments but wonder maybe there is an easier solution? Maybe @Alex Hübner or @James Fellows Yates can help? Thanks!

ivelsko (velsko@shh.mpg.de)
2020-09-23 17:42:42

*Thread Reply:* I’m having the same issue with DIAMOND-produced sam files. I’d also like to know if anyone has a solution

👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 17:50:46

*Thread Reply:* Hace you used the sparseSAM output? If so I would recommend turning that off

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 17:51:08

*Thread Reply:* If you didn't use that I need to check if I did anything special in a different project I was using them recently

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 17:52:37

*Thread Reply:* I don't think I did though

ivelsko (velsko@shh.mpg.de)
2020-09-23 17:54:05

*Thread Reply:* No, the issue w/the DIAMOND sam files is that it’s a pseudo-sam file, since they aren’t designed for protein alignments. @Nikolay Oskolkov did you run MALT in BLASTX mode? Do you also have protein alignments?

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-23 18:02:16

*Thread Reply:* @ivelsko I ran it in BLASTN mode for aligning DNA reads. @James Fellows Yates I did not use sparseSAM, no, here is how I ran it:

malt-run -at SemiGlobal -ssc -m BlastN -i fastqfile -o fastqfile.rma6 -a fastqfile.sam -t 20 -d maltdatabase

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 18:03:48

*Thread Reply:* Hmm, ok that looks pretty similar to what I use but I think without the soft flipping (iirc that's what the SSC flag does?). I'm having a day off today, but if you ping me tomorrow I'll check to see what I did

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 18:04:03

*Thread Reply:* Was there any particular error samtools was reporting?

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2020-09-23 18:08:39

*Thread Reply:* Thanks @James Fellows Yates, you are right, the issue seems to be related to the soft-clipping. I will check without the -ssc flag. Still strange that if you want to implement soft-clipping, you get a strange sam-file that can not be read by samtools

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-23 18:09:54

*Thread Reply:* Yeah, there are a few wierd things about the malt implementation. I would still try posting on the megan forum again. Semester is starting up again so maybe the Devs are back at work. It took me one or two attempts to get replies previously

👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-24 15:39:03

*Thread Reply:* yeah I don't see myself doing anything special in my code

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-24 15:39:20

*Thread Reply:* But I don't think I had to touch the cigar string

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-24 16:27:49

@channel Find here the draft of all the links/references posted during SPAAM2: https://docs.google.com/document/d/1oXS0MHg1DdB0xe3vlen5TEcC2SFZsp1aSwEOnK_soBM/edit?usp=sharing

Consider this a semi-annotated bibliography (I tried to put the context of each link, as far as I could remember/reconstruct from the chat), which we will bundle with the notes/slides from SPAAM2 and will make public.

Please feel free to make edits etc!

👍 Sterling Wright, Nikolay Oskolkov, Kun Huang, Katerina Guschanski, Nico Rascovan, Pooja Swali, aidanva
🤸‍♂️:skin_tone_4: Miriam Bravo
👏 Freddi Scheib, Katerina Guschanski
🙏 Ophélie Lebrasseur
Nico Rascovan (nicorasco@gmail.com)
2020-09-24 22:29:01

great! Very nice work James, thanks!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-30 16:49:03

@channel I'm just preparing the participant list for the notes/slides that we will be making publicly available (coming for your comments/corrections on Monday!)

We've used the Zoom records to take people who were present. *Is there anybody who shared someone else's connection and therefore didn't log in themselves?*

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-09-30 16:50:10

Yes, @Markella Moraitou

👍 Adrian Forsythe, James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-01 08:43:53

*Thread Reply:* Added

Åshild (Ash) (ashild.v@gmail.com)
2020-10-07 17:16:34

Hi @channel, Clio sent a follow-up email to the SPAAM2 workshop yesterday, be sure to check your spaam/junk folders for the email

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-07 17:18:05

*Thread Reply:* Real time Rapid markdown fixes, love it 😂

Åshild (Ash) (ashild.v@gmail.com)
2020-10-07 17:17:25

Below is the contents of the email: ```Dear all participants,

Thanks to you all again for taking part in the online meeting.

We are happy to share with you some of the meeting outputs:

If you wish to make any comment, change, correction, suggestion, addition to the notes and references, we encourage you to do so directly on the commentable files in this shared folder before Friday October 16. After this date, the files will be locked and uploaded onto Zenodo as pdf for long term archiving (and include a citable DOI).

Finally, we would really appreciate it if you could find 5 min to fill out our survey, and let us know how the next meeting could be improved, that would be very helpful for the next organising committee and the ancient metagenomics community in general. The deadline for the survey is also October 16 and you will find it here: https://forms.gle/Z6mM9Zt9QXxHvk637

Thanks again for your contribution

Best,

The Organization Team Standards, Precautions & Advances in Ancient Metagenomics 2

--

NEW DATES for the ISBA9 conference in Toulouse NOW June 1st-4th 2021, Don't miss it! International Symposium of Biomolecular Archaeology #ISBA9 https://isba9.sciencesconf.org/


Dr Clio Der Sarkissian CNRS Researcher Team AGES Laboratory AMIS Faculté de Médecine de Purpan 37 allée Jules Guesde 31000 Toulouse```

👍:skin_tone_4: Miriam Bravo
👍 Sterling Wright
😀 Jessica Hider
Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2020-10-14 15:54:24

Hi everyone Just a reminder that you have until this coming Friday October 16 to add your comments to the documents in the shared Google Drive folder: https://drive.google.com/drive/folders/1XPITeI2Sku9WScE85d4suyYXK1OyFgpU?usp=sharing

AND to fill out our survey: https://forms.gle/Z6mM9Zt9QXxHvk637

Thanks again for your contribution!

Best,

The Organization Team Standards, Precautions & Advances in Ancient Metagenomics 2

Google Docs
👍:skin_tone_4: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-20 15:24:49

@channel the comments are now closed, thanks for those who left them!

I'm pleased to announce the slides/notes from our discussions are now all available (and citable 😉 under a CC-BY license with a Zenodo DOI! ) here: https://github.com/SPAAM-community/spaam-event-notes! Be creative how you use them to make new projects, presentations etc!

The feedback from the survey has also been sared with the <#C01BL1HD57T|spaam3-organisers> who will use it to make the next event even better 💪

Last updated
<p>24 minutes ago</p>
👍 Ophélie Lebrasseur, Katerina Guschanski, aidanva, Emrah Kırdök, Anneke ter Schure, Pete Heintzman, Becky Cribdon, Nikolay Oskolkov, Shreya, Sterling Wright, Kun Huang
❤️ Ele
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-20 15:24:54

Thank again everyone!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-29 14:45:25

Did anyone get my email I just sent out about the SPAAM mailing list? My email is crapping out and saying it didn't send anything but it looks like some people may have got it?

🙌:skin_tone_3: Anna F.
👍 Abby Gancz, Nikolay Oskolkov
📬 Åshild (Ash), Shreya
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2021-01-29 14:45:37

i got it

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-29 14:45:47

OK good, thanks!

Sterling Wright (sterlingwright2016@utexas.edu)
2021-01-29 14:56:25

Got it as well

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-29 14:56:44

Awesome thanks!

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-21 16:13:46

Hi to those attending ISBA9! the conference platform will make virtual “lounge rooms” available for random chats and project-oriented discussions. This could be a good opportunity to meet with other members of the SPAAM community (in the limit of 20 participants though). If you’d like to set up a time to meet, let me know we can arrange that and announce the get-together.

🎉 aidanva, Åshild (Ash)
🙌:skin_tone_6: Miriam Bravo
👍 Maria Spyrou, Maria Lopopolo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-21 16:15:25

*Thread Reply:* YEESSSSSSS ❤️❤️❤️❤️

Nico Rascovan (nicorasco@gmail.com)
2021-05-22 00:16:20

Sounds like a very nice idea Clio!

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-25 15:07:01

OK, for those attending ISBA9, what about DAY 3 = THURSDAY JUNE, 3RD for a SPAAM get-together? Thursday looked good as people might be busy chatting with speakers on Day 2-Wednesday after the “Paleo-environment” session and on Day 4-Friday after the “Microbes & Pathogens” session. Now there are 2 options: 1) LUNCH meeting 12:3013:30 2) AFTERWORK meeting 19:0020:00

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-25 15:09:12

*Thread Reply:* I am doing an nf-core/eager live demo at 13:00_13:30...

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-25 15:09:40

*Thread Reply:* (but could still do it, and I leave halfway through)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:05:11

*Thread Reply:* @Clio Der Sarkissian I vote meeting at Pyrénées because how cool would it be to have a SPAAM meet up in the mountains!

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:07:35

*Thread Reply:* Not Cassoulet?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:07:49

*Thread Reply:* OK YES FOOD

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:07:52

*Thread Reply:* (I thought it was a place)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:08:06

*Thread Reply:* Holy shit that looks amazing

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:08:10

*Thread Reply:* Yes Cassoulet

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:10:08

*Thread Reply:* Pyrenees or Cassoulet? Pyrenees sounds more classy, but I’m not against a bit of fun.

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:10:42

*Thread Reply:* Did you also receive the e-mail to access your platform account?

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:12:10

*Thread Reply:* I thought we were supposed to get access in advance to fix texts so if you got it as well I might be working for nothing…

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:12:18

*Thread Reply:* Yes, I just logged in and that's how I found out about the different palces

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:12:31

*Thread Reply:* Well depends if you're feeling like gaining or burning energy 😆

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:12:35

*Thread Reply:* Bot hare good wit hme

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:13:17

*Thread Reply:* It is indeed a nice platform!

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:13:19

*Thread Reply:* aaargggh, OK, free time for me, not optimal English for us all, but let’s say it doesn’t matter as long as people understand

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:13:46

*Thread Reply:* Huh? Sorry I don't undersand...

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:14:52

*Thread Reply:* (ironicallly)

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:15:43

*Thread Reply:* thanks for explaining (not ironically)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:16:08

*Thread Reply:* Oh wait, slack didn't tell me about htis message:

> I thought we were supposed to get access in advance to fix texts so if you got it as well I might be working for nothing…

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:16:21

*Thread Reply:* Everything is understandanble to me so far

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:16:39

*Thread Reply:* good!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:16:40

*Thread Reply:* There is one page not translated but no-one would use it anyway

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 12:16:51

*Thread Reply:* which one?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:17:46

*Thread Reply:* Profile > A See my participant file

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:18:10

*Thread Reply:*

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:18:31

*Thread Reply:* But honestly 🤷

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:18:36

*Thread Reply:* You can work it out anyway

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:19:16

*Thread Reply:* Also noticed:

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:19:20

*Thread Reply:* In the chat box it's still french

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:19:55

*Thread Reply:* Then on hte 'online' page:

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:20:10

*Thread Reply:* But like I said, basically nothing people will ever use probably

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 12:20:16

*Thread Reply:* (or that they can't understand

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-26 13:11:04

*Thread Reply:* @Clio Der Sarkissian somethign that might be a bit more confusing:

On the right - when I started the private chat with Aida

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 13:21:41

*Thread Reply:* OK, thanks! I’ll let them know

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-25 15:07:20

Let me prepare a poll

Polly
2021-05-25 15:13:56

This polly is closed. @Clio Der Sarkissian has a polly for you!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-25 15:14:44

@channel SPAAM2 meet-up at ISBA9??? ☝️

Polly
2021-05-26 15:15:11

Your results are in! 🎉

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-05-26 16:54:57

19:00_20:00 CET on Thursday June 3rd on the ISBA9 platform it is then! I’ll let the committee know.

❤️ James Fellows Yates, aidanva, Maria Lopopolo, Ele, Nikolay Oskolkov, Zoé Pochon, Emrah Kırdök
👍 Maria Lopopolo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-02 17:26:29

@Clio Der Sarkissian is on TV!

👏 Nico Rascovan, Nikolay Oskolkov
🤸‍♀️:skin_tone_2: Anna F.
🎉 Alex Hübner, Ele
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-02 18:21:37

Well done @Miriam Bravo!

👍 Nikolay Oskolkov, Megan Michel, Emrah Kırdök, Valentina Zaro, Maria Lopopolo, Pooja Swali, Zandra Fagernäs, Maria Spyrou, ivelsko
💪 Alex Hübner, Nico Rascovan, Åshild (Ash), Ele
🥴 Miriam Bravo
Miriam Bravo (bravolomiriam@gmail.com)
2021-06-02 18:38:10

Thanks a lot!! 🙂

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-06-03 12:33:20

Great hair!

😆 James Fellows Yates
😁 Betsy Nelson
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-03 18:34:08

Sorry guys, I won't be able to join the meetup tonight due to family reasons. I hope you have a good time!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-04 11:54:32

Really nice talk @Lena G!!!!

👏 aidanva, Lena G, Emrah Kırdök, ivelsko, Maria Lopopolo, Betsy Nelson, Nikolay Oskolkov, Ele
Lena G (lena.granehall@gmail.com)
2021-06-04 15:16:09

*Thread Reply:* Thank you!

Nico Rascovan (nicorasco@gmail.com)
2021-06-04 12:00:08

It was really good!

Lena G (lena.granehall@gmail.com)
2021-06-04 15:16:23

*Thread Reply:* Thank you!

Nico Rascovan (nicorasco@gmail.com)
2021-06-04 12:00:12

I liked it a lot

Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-06-04 15:59:52

Congrats to all of you who presented a talk or a poster at ISBA9 and thanks for keeping discussions alive!

👏 James Fellows Yates, Nikolay Oskolkov, Maria Lopopolo, Ele
Maria Spyrou (spyrou@shh.mpg.de)
2021-06-04 16:17:09

Thanks so much for organising such a fantastic meeting, and hope to see all of you guys in person soon!

👏 James Fellows Yates, Nikolay Oskolkov, Ele, Christina Warinner
Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-06-04 16:30:06

Thanks! you’re always welcome in Toulouse!

👏 Nikolay Oskolkov, James Fellows Yates, aidanva, Zandra Fagernäs
🇫🇷 James Fellows Yates, Nikolay Oskolkov, Emrah Kırdök
❤️ Maria Spyrou, Nikolay Oskolkov, aidanva
🙌:skin_tone_6: Miriam Bravo
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2021-06-04 16:31:31

Fantastic event, really enjoyed, thanks a lot all the speakers and organizers!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-04 16:48:35

Congrats to both @Ele and @Zandra Fagernäs!!!

🎉 Miriam Bravo, Gunnar Neumann, Nikolay Oskolkov, Maria Lopopolo, Maria Spyrou, Pooja Swali
🤸‍♀️:skin_tone_2: Anna F.
:partyparrot: Anna F.
Anna F. (annakfos@gmail.com)
2021-06-04 16:52:24

*Thread Reply:* Amazing posters ladies! kudos! 🍾

Ele (eg715@york.ac.uk)
2021-06-07 10:56:41

*Thread Reply:* Gahh thank you ❤️

aidanva (aida.andrades@gmail.com)
2021-06-04 16:49:00

Congratulations!!

Emrah Kırdök (emrahkirdok@gmail.com)
2021-06-04 16:51:36

Thank you for the organizers and to the speakers. It was an informative event.

Maria Lopopolo (maria.lopopolo1989@gmail.com)
2021-06-04 17:21:08

Today (and every day really) it was mind blowing! Amazing talks, thank you very much!

👍 Christina Warinner
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-04 17:27:26
Maria Lopopolo (maria.lopopolo1989@gmail.com)
2021-06-04 17:30:00

*Thread Reply:* Starting with the good stuff I see, behind your laptop 💃

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-04 17:32:04

*Thread Reply:* That's entirely @aidanva 😂😂😂

Nico Rascovan (nicorasco@gmail.com)
2021-06-04 23:40:14

*Thread Reply:* Sugars, scissors and a control remote… who can resist…

😬 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-04 19:47:01

The cooking class was amazing @Clio Der Sarkissian thank you to ask the organisers!

👍 Christina Warinner
aidanva (aida.andrades@gmail.com)
2021-06-04 19:54:26

It was great!!! Thank you @Clio Der Sarkissian !! Such an awesome idea !

👍 Christina Warinner
Clio Der Sarkissian (clio.dersarkissian@gmail.com)
2021-06-07 09:10:03

Glad you had a good time! we also did!

Ele (eg715@york.ac.uk)
2021-06-07 10:57:28

*Thread Reply:* Absolutely loved it Clio - really well done 👏👏👏

pierrespc (pierrespc@gmail.com)
2021-06-16 12:14:54

Hi everybody. Thanks for this slack. I am not sure I have to ask in this specific channel concerning some issues I face with nf-core/eager

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-16 12:16:16

Hi @pierrespc - genreal questions for SPAAM people is better on #general (this channel is just for discussion about the SPAAM2 workshop from last year). However if you have specific questions about eager, please join the nf-core slack: https://nf-co.re/join and join the #eager channel there 🙂

nf-co.re
pierrespc (pierrespc@gmail.com)
2021-06-16 12:16:45

Great Thanks!

pierrespc (pierrespc@gmail.com)
2021-06-16 12:16:52

see you there then

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-16 12:17:53

But good point: I will be *closing* this channel when <#C025AP39256|spaam3-open> happens in September! So please direct general discussions to #general, but of course join <#C025AP39256|spaam3-open> for discussions about the next event 🙂

🙌 Maria Lopopolo
ivelsko (velsko@shh.mpg.de)
2021-09-10 15:01:30

Hello @channel! The SPAAM2 organizers are pleased to announce that the manuscript draft based on discussions at SPAAM2 last September is now assembled. A major theme we saw throughout the conference and the reviews that were shared with us was that many people struggle to convince people outside the field of the authenticity and relevance of their work. To attempt to ease this issue, we assembled a short opinion piece detailing critical points in ancient metagenomics to assist peer reviewers understand and interpret ancient data.

We invite all SPAAM2 participants to read through and leave comments over the next 2 weeks (last day September 24th). We especially hope the sdeaDNA people will check that we didn't miss anything important as none of us work specifically in that area

Please know that everyone who sent us reviews or review summaries, and everyone who has comments on this draft, will be mentioned by name in the Acknowledgments. If you have questions feel free to message or email us. Here's the link: https://docs.google.com/document/d/17Hfxwsr12_VOsS0cMQn_kfvUnzDQYTidckymrqUqHVc/edit?usp=sharing

👍 Nikolay Oskolkov, Sterling Wright
Ele (eg715@york.ac.uk)
2021-09-19 17:08:06

*Thread Reply:* No comments, but just wanted to say it was a great read, well don everyone. Table 2 is a great idea!

Zoé Pochon (zoe.pochon@gmail.com)
2021-10-04 16:35:24

*Thread Reply:* Same ! It was a really nice recap for someone who just joined the field. Plus, I love figure 2 🤩!

Pete Heintzman (peteheintzman@gmail.com)
2021-09-10 16:25:04

@ivelsko @James Fellows Yates -- have added a few comments to make it more sedaDNA friendly. 🙂

❤️ James Fellows Yates
👍 Åshild (Ash)
ivelsko (velsko@shh.mpg.de)
2021-09-10 16:30:20

*Thread Reply:* Thanks!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-10 16:48:13

*Thread Reply:* Thank you very much

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2021-09-16 13:55:43

Great manuscript @ivelsko, @James Fellows Yates and other guys, I read it with lot of interest and added a few comments on computational data analysis challenges, hopefully you will find them useful.

❤️ James Fellows Yates, Arumi Mendoza
:meow_party: Anna F., Diana Ivette Cruz Dávalos
🙌 Jessica Hider
ivelsko (velsko@shh.mpg.de)
2021-09-16 13:58:40

*Thread Reply:* Great, thanks!

Jessica Hider (hiderj@mcmaster.ca)
2021-09-23 20:53:10

Really enjoyed reading this @ivelsko @James Fellows Yates, well done. I just wanted to write the is awesome everywhere, but felt that would be a little annoying. So I'll say it here instead!

❤️ James Fellows Yates, Sterling Wright, Adrian Forsythe
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-23 21:17:25

*Thread Reply:* Thank you!

ivelsko (velsko@shh.mpg.de)
2021-09-24 09:44:20

*Thread Reply:* Thanks!

Ophélie Lebrasseur (ophelie.lebrasseur@liverpool.ac.uk)
2021-09-24 17:22:09

Great paper, I really enjoyed reading it too - it's very clear and easy to read. I've added a few comments based on personal experience working with epidemiologists, but see how you guys feel about them ^^

❤️ James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-24 17:45:36

*Thread Reply:* Thank you!

ivelsko (velsko@shh.mpg.de)
2021-09-26 18:43:29

*Thread Reply:* Thanks!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-27 09:46:21

@Pete Heintzman @Nikolay Oskolkov @Jessica Hider @Katerina Guschanski @Ophélie Lebrasseur I've gone through and made suggestions based on your comments. Please let me know if they work for you (@Clio Der Sarkissian @Alex Hübner @irinavelsko @Åshild (Ash) @Anna F. as well!)

✅ Pete Heintzman
👍 Jessica Hider
Ophélie Lebrasseur (ophelie.lebrasseur@liverpool.ac.uk)
2021-09-27 11:18:02

@James Fellows Yates, Just looked through and I'm happy with all the changes/suggestions you've made. Thank you 😊

❤️ James Fellows Yates
Miriam Bravo (bravolomiriam@gmail.com)
2021-09-29 06:55:20

@irinavelsko, @James Fellows Yates and the rest of SPAAM2 organizers, I also enjoyed reading your article since it is a very much needed information in the field. I made a few irrelevant suggestions 🙂. Thanks for sharing !

❤️ James Fellows Yates
ivelsko (velsko@shh.mpg.de)
2021-09-29 09:09:24

*Thread Reply:* Thanks!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-29 10:04:25

*Thread Reply:* Thanks!

aidanva (aida.andrades@gmail.com)
2021-10-07 08:45:27

Hi! I just had the chance to go through the manuscript, and what a nice read it is! Left a few comments, probably all irrelevant. Great work SPAAM2 organisers!

❤️ James Fellows Yates, Åshild (Ash)
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-11 07:36:01

@channel hive mind, can you give me a list of papers that involve wet lab method development for ancient Metagenomics (either papers specifically addressing it, or studies which included a method dev component)?

The ones from my head are just ones which I've been in the sphere of, so I suspect I'm missing some as wet lab is not my expertise.

Current ones: Warinner 2014, Hagan 2020, Brealey 2020, fagernäs 2020, Farrer 2021

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-11 11:29:20

tumbleweed

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-11 11:29:27

Have I really got everything?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-11 11:32:07

Ah Slon 2017 for seidment

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-11 11:38:49

Oh and Farrer 2021

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-11 11:40:35

And @Linda Armbrecht’s marine sedaDNAcapture one

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-11 11:47:09

@Clio Der Sarkissian did your shell one also include some extraction optiomisation or something 🤔