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Maxime Borry (maxime.borry@gmail.com)
2020-09-24 17:39:15

@channel To follow up on this, the authors of the LEMMI benchmark would be willing to integrate an ancient DNA challenge dataset. See: https://gitlab.com/ezlab/lemmi/-/issues/5#note_417925884

I have no experience with Gargammel, because I always used the sequence simulator that I wrote (ADRSM - https://github.com/maxibor/adrsm), but if someone wants to give it a try with Gargammel, feel free ! Otherwise, I would propose a dataset simulated with ADRSM

maxibor/adrsm
<p>Ancient DNA Read Simulator for Metagenomic </p>
Stars
<p>1</p>
Language
<p>HTML</p>
<a href="https://github.com/maxibor/adrsm">maxibor/adrsm</a>
GitLab
Adding new aDNA challenge dataset (#5) · Issues · ezlab / lemmi
Hi, As the field of ancient DNA (aDNA) metagenomics is developping, we face the same challenge of method benchmarking. However, aDNA data are a bit different compared to modern DNA:...
Author
Maxime Borry
Original URL: https://gitlab.com/ezlab/lemmi/-/issues/5#note_417925884
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 17:44:30

I have a flexible simulator that uses fragSim, deamSim and adaptSim from gargammel that generates synthetic microbial communities, in addition it tracks damage in each codon for protein based benchmarks

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 17:45:01

I haven’t make it open yet, still benchmarking it

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 17:46:12

it can take biom files with the profile of your samples, the mapdamage2 misincorporation.txt file and generates datasets to fine tune your analyses

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 17:46:52

once I make it open we can play around a create few test datasets to play around

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