James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-19 16:59:20
*Thread Reply:* This is how it should be
Antonio Fernandez-Guerra
(antonio@metagenomics.eu)
2020-08-19 17:05:28
*Thread Reply:* IN theory, any data at ENA/SRA should not contain technical sequences https://ena-docs.readthedocs.io/en/latest/submit/fileprep/reads.html#fastq-format and soon SRA will remove qualities from fastq
Antonio Fernandez-Guerra
(antonio@metagenomics.eu)
2020-08-19 17:06:03
*Thread Reply:* well they have a call to ask the community
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-19 17:06:28
*Thread Reply:* Yes, unfortunately people ignore that -.-. surprised thats not checked for actually.
Yes I saw...I hope ena doesn't follow suit
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-19 17:06:42
*Thread Reply:* Terrible for us
Antonio Fernandez-Guerra
(antonio@metagenomics.eu)
2020-08-19 17:06:57
*Thread Reply:* They have CRAM as an alternative
Antonio Fernandez-Guerra
(antonio@metagenomics.eu)
2020-08-19 17:07:19
*Thread Reply:* let’s see, the community is not so happy
Antonio Fernandez-Guerra
(antonio@metagenomics.eu)
2020-08-19 17:38:24
i would keep in the standard terms: https://www.nature.com/articles/nbt.3893
Nature Biotechnology
Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed.
Original URL: https://www.nature.com/articles/nbt.3893
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-20 09:42:23
https://github.com/SPAAM-workshop/AncientMetagenomeDir/pull/146
}
<p><strong>Pull Request</strong></p>
<p>Adds new column for single-genome hostassociated list to allow non-raw data sequences (e.g. when only consesnus sequence uploaded to GenBank).</p>
<p>Definitions are as originally described in the slack discussion.</p>
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-20 12:01:14
*Thread Reply:* We have the two siseus, right?
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-20 12:01:23
*Thread Reply:* Oh you mean with the keys
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-20 12:01:29
*Thread Reply:* I've already sneakly fixed that a couple days ago 😉
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-20 12:21:34
<p>```
project<em>name publication</em>year publication<em>doi site</em>name latitude longitude geo<em>loc</em>name sample<em>name sample</em>host sample<em>age sample</em>age<em>doi singlegenome</em>domain singlegenome<em>species material collection</em>date archive data<em>type archive</em>accession
Schuenemann2013 2013 10.1126/science.1238286 Sigtuna 59.618 17.726 Sweden 3077 Homo sapiens 900 10.1126/science.1238286 bacteria Mycobacterium leprae bone NA SRA raw SRS418834
Schuenemann2013 2013 10.1126/science.1238286 Odense St. Jørgen cemetery 55.399 10.406 Denmark Jorgen<em>625 Homo sapiens 700 10.1126/science.1238286 bacteria Mycobacterium leprae tooth NA SRA raw SRS418854
Schuenemann2013 2013 10.1126/science.1238286 Refshale 56.193 9.394 Denmark Refshale</em>16 Homo sapiens 900 10.1126/science.1238286 bacteria Mycobacterium leprae tooth NA SRA raw SRS419262,SRS418858,SRS418859
Schuenemann2013 2013 10.1126/science.1238286 St. Mary Magdalene leprosarium, Winchester 51.059 -1.308 United Kingdom SK2 Homo sapiens 700 10.1126/science.1238286 bacteria Mycobacterium leprae bone NA SRA raw SRS418843
Schuenemann2013 2013 10.1126/science.1238286 St. Mary Magdalene leprosarium, Winchester 52.059 -1.308 United Kingdom SK8 Homo sapiens 900 10.1126/science.1238286 bacteria Mycobacterium leprae tooth NA SRA raw SRS418845
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Odense St. Jørgen cemetery 55.399 10.406 Denmark Jorgen<em>404 Homo sapiens 700 10.1371/journal.ppat.1006997 bacteria Mycobacterium leprae tooth NA ENA raw ERS1574247
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Odense St. Jørgen cemetery 55.399 10.406 Denmark Jorgen</em>427 Homo sapiens 800 10.1371/journal.ppat.1006997 bacteria Mycobacterium leprae tooth NA ENA raw ERS1574249
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Odense St. Jørgen cemetery 55.399 10.406 Denmark Jorgen<em>507 Homo sapiens 800 10.1371/journal.ppat.1006997 bacteria Mycobacterium leprae tooth NA ENA raw ERS1574253
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Odense St. Jørgen cemetery 55.399 10.406 Denmark Jorgen</em>533 Homo sapiens 900 10.1371/journal.ppat.1006997 bacteria Mycobacterium leprae tooth NA ENA raw ERS1574254
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Odense St. Jørgen cemetery 55.399 10.406 Denmark Jorgen<em>722 Homo sapiens 700 10.1371/journal.ppat.1006997 bacteria Mycobacterium leprae tooth NA ENA raw ERS1574259
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Odense St. Jørgen cemetery 55.399 10.406 Denmark Jorgen</em>749 Homo sapiens 700 10.1371/journal.ppat.1006997 bacteria Mycobacterium leprae tooth NA ENA raw ERS1574262
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Szentes-Kistőke 46.715 20.281 Hungary SK11 Homo sapiens 1300 10.1016/j.meegid.2015.02.001 bacteria Mycobacterium leprae bone NA SRA raw SRS2667046
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Necropoli Vicenne Campochiaro 41.564 14.498 Italy T18 Homo sapiens 1300 10.1016/j.meegid.2015.02.001 bacteria Mycobacterium leprae bone NA SRA raw SRS2667044
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Prušánky 48.831 16.982 Czech Republic Body 188 Homo sapiens 1100 10.1016/j.meegid.2015.02.001 bacteria Mycobacterium leprae bone NA SRA raw SRS2667047
Schuenemann2018 2018 10.1371/journal.ppat.1006997 Great Chesterford 52.063 0.193 United Kingdom GC96 Homo sapiens 1500 10.1371/journal.pone.0124282 bacteria Mycobacterium leprae bone NA SRA raw SRS2667045
Warinner2014 2014 10.1038/ng.2906 Dalheim 51.565 8.84 Germany G12 Homo sapiens 900 10.1038/ng.2906 bacteria Tannerella forsythia tooth NA SRA raw SRS473747,SRS473746,SRS473748,SRS473749,SRS473750
Bos2014 2014 10.1038/nature13591 El Yaral -17.41 -71.092 Peru 64 Homo sapiens 700 10.1038/nature13591 bacteria Mycobacterium pinnipedii bone NA SRA raw SRS592075
Bos2014 2014 10.1038/nature13591 El Algodonal -17.583 -71.21 Peru 58 Homo sapiens 800 10.1038/nature13591 bacteria Mycobacterium pinnipedii bone NA SRA raw SRS591992
Bos2014 2014 10.1038/nature13591 Chiribaya Alta -17.621 -71.269 Peru 54 Homo sapiens 800 10.1038/nature13591 bacteria Mycobacterium pinnipedii bone NA SRA raw SRS591994
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 Rasshevatskiy 45.569 41.03 Russia RK1001 Homo sapiens 4700 10.1016/j.cub.2017.10.025 bacteria Yersinia pestis tooth NA ENA raw ERS1892069
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 Beli Manastir-Popova zemlja 45.77 18.61 Croatia GEN72 Homo sapiens 4700 10.1016/j.cub.2017.10.025 bacteria Yersinia pestis tooth NA ENA raw ERS1892068
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 Gyvakarai 55.913 24.89 Lithuania Gyvakarai1 Homo sapiens 4500 10.1016/j.cub.2017.10.025 bacteria Yersinia pestis tooth NA ENA raw ERS1892064
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 Kunila 58.616 23.796 Estonia KunilaII Homo sapiens 4400 10.1016/j.cub.2017.10.025 bacteria Yersinia pestis tooth NA ENA raw ERS1892065
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 Haunstetten Unterer Talweg 85 48.318 10.891 Germany 1343UnTal85 Homo sapiens 4200 10.1371/journal.pone.0139705 bacteria Yersinia pestis tooth NA ENA raw ERS1892067
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 Haunstetten Postillionstrasse 6 48.308 10.893 Germany 6Post Homo sapiens 3900 10.1371/journal.pone.0139705 bacteria Yersinia pestis tooth NA ENA raw ERS1892066
Spyrou2018 2018 10.1038/s41467-018-04550-9 Mikhailovsky II burial site 53.2 50.2 Russia RT5 Homo sapiens 3800 10.1038/s41467-018-04550-9 bacteria Yersinia pestis tooth NA ENA raw ERS2106903
Spyrou2018 2018 10.1038/s41467-018-04550-9 Mikhailovsky II burial site 53.2 50.2 Russia RT6 Homo sapiens 3800 10.1038/s41467-018-04550-9 bacteria Yersinia pestis tooth NA ENA raw ERS2106904
Rascovan2019 2019 10.1016/j.cell.2018.11.005 Gökhem 94:1, Frälsegården 58.173 13.407 Sweden Gok2 Homo sapiens 4900 10.1016/j.cell.2018.11.005 bacteria Yersinia pestis tooth NA ENA raw ERS434180
Rasmussen2015 2015 10.1016/j.cell.2015.10.009 Sope 59.408 27.026 Estonia RISE00 Homo sapiens 4400 10.1038/nature14507 bacteria Yersinia pestis tooth NA ENA raw ERS848971
Rasmussen2015 2015 10.1016/j.cell.2015.10.009 Chociwel 50.796 17.094 Poland RISE139 Homo sapiens 4000 10.1038/nature14507 bacteria Yersinia pestis tooth NA ENA raw ERS848972
Rasmussen2015 2015 10.1016/j.cell.2015.10.009 Bulanovo 52.453 55.16 Russia RISE386 Homo sapiens 4000 10.1038/nature14507 bacteria Yersinia pestis tooth NA ENA raw ERS848973
Rasmussen2015 2015 10.1016/j.cell.2015.10.009 Kapan 39.2 46.4 Armenia RISE397 Homo sapiens 2900 10.1038/nature14507 bacteria Yersinia pestis tooth NA ENA raw ERS848974
Rasmussen2015 2015 10.1016/j.cell.2015.10.009 Kytmanovo 53.456 85.447 Russia RISE505 Homo sapiens 3600 10.1038/nature14507 bacteria Yersinia pestis tooth NA ENA raw ERS848975
Rasmussen2015 2015 10.1016/j.cell.2015.10.009 Bateni 54.584 90.775 Russia RISE509 Homo sapiens 4800 10.1038/nature14507 bacteria Yersinia pestis tooth NA ENA raw ERS848976
Rasmussen2015 2015 10.1016/j.cell.2015.10.009 Bateni 54.584 90.775 Russia RISE511 Homo sapiens 4700 10.1038/nature14507 bacteria Yersinia pestis tooth NA ENA raw ERS848977
Yu2020 2020 10.1016/j.cell.2020.04.037 Glazkovskoe Predmestie Site 52.279 104.251 Russia GLZ001 Homo sapiens 4300 10.1016/j.cell.2020.04.037 bacteria Yersinia pestis tooth NA ENA raw ERS4540520
Yu2020 2020 10.1016/j.cell.2020.04.037 Glazkovskoe Predmestie Site 52.279 104.251 Russia GLZ002 Homo sapiens 4400 10.1016/j.cell.2020.04.037 bacteria Yersinia pestis tooth NA ENA raw ERS4540521
Devault2017 2017 10.7554/eLife.20983 Troy 39.953 26.236 Turkey Nod1 Homo sapiens 800 10.7554/eLife.20983 bacteria Gardnerella vaginalis calcified nodule NA SRA raw SRS1779841,SRS1779840
Devault2017 2017 10.7554/eLife.20983 Troy 39.953 26.236 Turkey Nod1 Homo sapiens 800 10.7554/eLife.20983 bacteria Staphylococcus saprophyticus calcified nodule NA SRA raw SRS1779841,SRS1779840
Devault2017 2017 10.7554/eLife.20983 Troy 39.953 26.236 Turkey Nod2 Homo sapiens 800 10.7554/eLife.20983 bacteria Gardnerella vaginalis calcified nodule NA SRA raw SRS1779846,SRS1779844
Devault2…</p>
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-20 12:57:50
*Thread Reply:* Fixed, check again ❤️
aidanva
(aida.andrades@gmail.com)
2020-08-20 14:56:10
*Thread Reply:* approved, there is some conflicts though
Åshild (Ash)
(ashild.v@gmail.com)
2020-08-21 16:00:26
Can I rename to “single-genome-ancientmetagenomedir”? Reason why I didn’t start with “ancientmetagenomedir” is bc it now looks like. this on my sidebar 😉 😉
Åshild (Ash)
(ashild.v@gmail.com)
2020-08-21 16:07:12
*Thread Reply:* how? can’t seem to find on google
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-21 16:07:22
*Thread Reply:* Don't worry, fine it
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-21 16:08:54
*Thread Reply:* It was the other channel, maybe not visible as you weren't there
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-21 16:09:16
*Thread Reply:* Sorry I mean the AncientMetagenomeDir-environment slack channel
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-21 16:09:38
*Thread Reply:* <#C018UBC9T47|dir-environmental> <- which is there. Would be the same procedure as for this one
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-24 14:13:58
Another question, as @aidanva brought up/predicted before, but it has now come up in https://github.com/SPAAM-workshop/AncientMetagenomeDir/pull/170 from @Becky Cribdon, in de Dios 2020 they report hits to a eukaryotic pathogen but they only recover/analyses a mt genome for one of the pathogens
}
<p><strong>Pull Request</strong></p>
<p>This PR is for a</p>
<p>☑︎ <#new-publication|New Publication(s)>
☐ <#correction|Correction></p>
<p>For the follow list (s)</p>
<p>☐ ancientmetagenome-anthropogenic (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-anthropogenic">README</a>)
☐ ancientmetagenome-environmental (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-environmental">README</a>)
☐ ancientmetagenome-hostassociated (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-hostassociated">README</a>)
☑︎ ancientsinglegenome-hostassociated (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientsinglegenome-hostassociated">README</a>)</p>
<p><strong>New Publication</strong>
<strong>Publication Information</strong></p>
<p>This pull request is to add samples from the following publication(s):</p>
<p>de-Dios 2020 10.1016/j.meegid.2020.104209 To close <a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/issues/65">#65</a></p>
<p><strong>Checklist</strong></p>
<p>☑︎ Publication is published (preprints currently not accepted)?
☑︎ Checked the publication is not already in the database?
☑︎ Checked samples in this publication are not previously published <em>data</em> (newly re-sequenced metagenomes are OK!)?
☑︎ Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
☑︎ Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
☑︎ (If applicable) Updated the JSON files under <code>/assets/enums</code> with new categories (e.g. material or archive)?
☑︎ Does your PR pass validation checks?
☑︎ Changelog is updated?</p>
<p>If you do not know how to check errors in failed validation checks, expand here</p>
<ol><li>Press 'details' next to the failed check.</li><li>Expand the <code>test ancient &lt;list&gt;</code> line with the red X next to it.</li><li>Scroll to the bottom of the log, and look for a <code>DatasetValidationError</code> (usually the last line).</li><li>Read the error, and fix accordingly. Check the README for a given list for more guidance. If in doubt, ask!</li>
</ol>
<p><strong>Correction</strong></p>
<p>This PR is for</p>
<p>☐ ancientmetagenome-hostassociated
☐ ancientsinglegenome-hostassociated
☐ ancientmetagenome-environmental
☐ ancientmetagenome-anthropogenic</p>
<p><strong>Reference</strong></p>
<p>This pull request is to correct samples from the following publication(s):</p>
<p><strong>Description</strong></p>
<p>The issue is:</p>
<p><strong>Checklist</strong></p>
<p>☐ Checked the corrected entries follow conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)
☐ Does your PR pass validation checks?
☐ Changelog is updated?</p>
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-25 17:05:05
*Thread Reply:* They are so fed up of the whole thing they forget
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-25 17:05:34
*Thread Reply:* (speaking from experience)
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-25 17:05:47
*Thread Reply:* shifty eyes
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-25 21:59:38
Thanks @Miriam Bravo for the PR for Kerudin! I've made a few comments on the the PR, https://github.com/SPAAM-workshop/AncientMetagenomeDir/pull/195
}
<p><strong>Pull Request</strong></p>
<p>This PR is for a</p>
<p>☑︎ <#new-publication|New Publication(s)>
☐ <#correction|Correction></p>
<p>For the follow list (s)</p>
<p>☐ ancientmetagenome-anthropogenic (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-anthropogenic">README</a>)
☐ ancientmetagenome-environmental (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-environmental">README</a>)
☐ ancientmetagenome-hostassociated (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-hostassociated">README</a>)
☑︎ ancientsinglegenome-hostassociated (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientsinglegenome-hostassociated">README</a>)</p>
<p><strong>New Publication</strong>
<strong>Publication Information</strong></p>
<p>This pull request is to add samples from the following publication(s):</p>
<p><strong>Checklist</strong></p>
<p>☑︎ Publication is published (preprints currently not accepted)?
☑︎ Checked the publication is not already in the database?
☑︎ Checked samples in this publication are not previously published <em>data</em> (newly re-sequenced metagenomes are OK!)?
☑︎ Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
☑︎ Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
☐ (If applicable) Updated the JSON files under <code>/assets/enums</code> with new categories (e.g. material or archive)?
☐ Does your PR pass validation checks?
☑︎ Changelog is updated?</p>
<p>If you do not know how to check errors in failed validation checks, expand here</p>
<ol><li>Press 'details' next to the failed check.</li><li>Expand the <code>test ancient &lt;list&gt;</code> line with the red X next to it.</li><li>Scroll to the bottom of the log, and look for a <code>DatasetValidationError</code> (usually the last line).</li><li>Read the error, and fix accordingly. Check the README for a given list for more guidance. If in doubt, ask!</li>
</ol>
<p><strong>Correction</strong></p>
<p>This PR is for</p>
<p>☐ ancientmetagenome-hostassociated
☐ ancientsinglegenome-hostassociated
☐ ancientmetagenome-environmental
☐ ancientmetagenome-anthropogenic</p>
<p><strong>Reference</strong></p>
<p>This pull request is to correct samples from the following publication(s):</p>
<p><strong>Description</strong></p>
<p>The issue is:</p>
<p><strong>Checklist</strong></p>
<p>☐ Checked the corrected entries follow conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)
☐ Does your PR pass validation checks?
☐ Changelog is updated?</p>
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2020-08-27 09:30:30
Could someone review this: https://github.com/SPAAM-workshop/AncientMetagenomeDir/pull/216
Fixes Maixner and changes versioning system to a vYY.MM based system, as I think this is more readable for humans when we will have time based releases
<p><strong>Pull Request</strong></p>
<p>This PR is for a</p>
<p>☐ <#new-publication|New Publication(s)>
☐ <#correction|Correction></p>
<p>For the follow list(s)</p>
<p>☐ ancientmetagenome-anthropogenic (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-anthropogenic">README</a>)
☐ ancientmetagenome-environmental (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-environmental">README</a>)
☐ ancientmetagenome-hostassociated (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-hostassociated">README</a>)
☐ ancientsinglegenome-hostassociated (<a href="https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientsinglegenome-hostassociated">README</a>)</p>
<p><strong>New Publication</strong>
<strong>Publication Information</strong></p>
<p>This pull request is to add samples from the following publication(s):</p>
<p>This is to close</p>
<p><strong>Checklist</strong></p>
<p>☐ Publication is published (preprints currently not accepted)?
☐ Checked the publication is not already in the database?
☐ Checked samples in this publication are not previously published <em>data</em> (newly re-sequenced metagenomes are OK!)?
☐ Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
☐ Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
☐ (If applicable) Made a separate PR to add new categories to controlled lists (stored unnder <code>/assets/enums</code>, e.g. material or archive)? If so:
☐ Does your PR pass validation checks?
☐ Changelog is updated?</p>
<p>If you do not know how to check errors in failed validation checks, expand here</p>
<ol><li>Press 'details' next to the failed check.</li><li>Expand the <code>test ancient &lt;list&gt;</code> line with the red X next to it.</li><li>Scroll to the bottom of the log, and look for a <code>DatasetValidationError</code> (usually the last line).</li><li>Read the error, and fix accordingly. Check the README for a given list for more guidance. If in doubt, ask!</li>
</ol>
<p><strong>Correction</strong></p>
<p>This PR is for</p>
<p>☐ ancientmetagenome-hostassociated
☑︎ ancientsinglegenome-hostassociated
☐ ancientmetagenome-environmental
☐ ancientmetagenome-anthropogenic</p>
<p><strong>Reference</strong></p>
<p>This pull request is to correct samples from the following publication(s): Maixner 2016</p>
<p><strong>Description</strong></p>
<p>The issue is: the singlegenome list should indeed be that. The authors reconstructed a genome by combining all samples and should be listed as such.</p>
<p>This also includes a switch to Calendar Versioning rather than SemVar as this makes more sense for human-readable database updates.</p>
<p><strong>Checklist</strong></p>
<p>☐ Checked the corrected entries follow conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)
☐ Does your PR pass validation checks?
☐ Changelog is updated?</p>
Åshild (Ash)
(ashild.v@gmail.com)
2020-08-31 14:08:49
*Thread Reply:* Or, rather it is an issue and Aida is already assigned to it 🙂
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2021-06-24 10:07:43
*Thread Reply:* Not definitevely
aidanva
(aida.andrades@gmail.com)
2021-11-09 08:52:04
*Thread Reply:* I did a quick check, it seems that the library was selected only for siRNA. I would say that that’s not a complete genome and I’m not sure how metagenomic it is. So I wouldn’t include it at the moment, but it make me think: did we add other RNA studies before?
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2021-11-09 09:59:33
*Thread Reply:* Good question
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2021-11-09 09:59:43
*Thread Reply:* I think there was a couple yes 🤔
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2021-11-09 10:00:48
*Thread Reply:* Looks pretty complete genome to me?
Åshild (Ash)
(ashild.v@gmail.com)
2021-11-09 14:36:55
*Thread Reply:* I’ve only had time to look at it very briefly, but I think we should add it. We have added other RNA genomes before and since it is at such high coverage, as James points out, I don’t see any reason not to add it
aidanva
(aida.andrades@gmail.com)
2021-11-10 09:41:56
*Thread Reply:* I agree, I missread it, not that I look at it more in depth we should add it.
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2021-11-09 08:34:44
https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8553777/
PubMed Central (PMC)
Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. ...
Original URL: https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8553777/
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2021-12-08 21:03:47
https://www.sciencedirect.com/science/article/pii/S2666517421000699#sec0013
sciencedirect.com
: Dental pulp, encapsulating a blood drop, could be used to diagnose pathogen bacteraemia in archaeological materials using DNA-based techniques. We q…
Original URL: https://www.sciencedirect.com/science/article/pii/S2666517421000699#sec0013
Kelly Blevins
(blevinske1@gmail.com)
2021-12-09 10:57:13
*Thread Reply:* Is any one else’s mind blown that bacteria from 100-year-old teeth from non-permafrost burial conditions could be cultured?
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2022-05-26 19:03:16
Y/N for the TB hits?
https://www.nature.com/articles/s41598-022-10899-1
Nature
Scientific Reports - Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD
Original URL: https://www.nature.com/articles/s41598-022-10899-1
James Fellows Yates
(james_fellows_yates@eva.mpg.de)
2022-05-27 20:45:57
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9090925/
PubMed Central (PMC)
The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9090925/
