Yannis Nevers
@Why_NeverS
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Post-doctoral researcher interested in Comparative Genomics.
France
Joined July 2016
RT @TheBGAcademy: Session 24: OMA/OMArk is starting in 1 hour (14:00 UTC). To join in the session, jump over to our discord at: https://t.….
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RT @SinaMajidian: In half an hour, Yannis Nevers @Why_NeverS and I will be talking about OMA and OMArk for homology exploration and gene….
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RT @TheBGAcademy: Another great day of sessions tomorrow with:. T2T assemblies w/ Verko - @sergekoren at 6am UTC.Genomes on a Tree - @Cibe….
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RT @SinaMajidian: Interested in minimizers and their applications in genomics? Check out our review. When Less is More:.
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RT @dpkyadav23: An insightful talk by @cdessimoz explaining OMArk, a work led by @Why_NeverS, at #ECCB2024. @dbc_unil .
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RT @richard_durbin: Gene Myers just released super fast whole genome aligner He and @c1zhou and I have lots of ide….
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RT @SinaMajidian: 📢CALL FOR ABSTRACTS📢. 🌟Abstract submission is now open for the Quest for Orthologs meeting #QFO8 which will be held at t….
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RT @SinaMajidian: Heading to Paris to give a talk on FastOMA and Read2tree for orthology and phylogeny inference! Thursday 7th, at 2pm in….
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RT @erga_biodiv: #ERGABlog | New Interview with @ADennis1980 - Learn about her views on the critical process of genome #annotation, the ne….
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RT @rmwaterhouse: The repertoire of STING-regulated #genes in ten Drosophila 🪰 species spanning 50 million years of #evolution
https://t.co….
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OMArk is available on GitHub (, and you can also install it with PyPi ( or Bioconda (. Please give it a try!.
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We also answer a very relevant question: does the source of annotations in the underlying OMA database bias our evaluation? Answer: It does make similar annotations look slightly better but the effect is negligible. High-quality proteomes will still appear as high quality!.
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Thanks to insightful comments from reviewers we added new analyses, including new benchmarking of simulated data for fragmented and fused gene model detection!.
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What has changed since our preprint came out? First, we improved our k-mer placements algorithms! Genes with no homolog support will now be classified as Unknown rather than Inconsistent. This leads to better results in our benchmarking as well!.
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Here is an in-depth diveinto how it works: (click to see the thread).
2) OMArk reports not only what is expected to be in a gene set (completeness assessment), but also what is *not* expected to be there, such as contamination or other dubious sequences (consistency assessment). (More about how we do it in tweet 8.)
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If you are not familiar with it, OMArk is special in that it does both a completeness and an overall consistency assessment. The latter can help you flag and investigate genes that have limited support from homology to close species! Be it contamination or spurious gene models.
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Our OMArk paper is finally out at @NatureBiotech! I am excited to share the final results of our work with @Gloveface @cdessimoz @VictorRossier @DessimozLab. OMArk is a one-stop shop for eukaryotic genome annotation assessment. Link : (🧵).
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RT @ISBSIB: How to evaluate the quality of a genome annotation? Introducing #OMArk, a groundbreaking tool by SIB’s @Why_Nevers & @Dessimoz….
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