L’édition #jobim2022 est maintenant terminée. Merci à tous de votre participation 👏 Félicitations à tous les intervenants et un grand bravo à l’équipe organisatrice 🎉

Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Ragnar {Groot Koerkamp} 🦋 and I extended the seed heuristic to exact alignment of long (Mbps) erroneous (≤15%) sequences. The empyrical near-linear runtime makes our aligner A*PA 250x faster than Edlib and WFA on synthetic data, and looks promising on human data. biorxiv.org/cgi/content/sh…

Recently, I wrote a bunch of Zotero tutorials that went (mildly) viral on #AcademicTwitter. Thought I'd put them all together so folks can find them easily. So, here goes 👇 Zotero 101: A meta-thread 🧵 Retweet to share it with your friends/colleagues.

Wonderful #Seqbim2022 in Bordeaux, thanks to the organizers! By the way, did I mention that Lille will host the GDR BIM days in November 2023, that will be joint with #Seqbim23 ?

mapquik: Efficient low-divergence mapping of long reads in minimizer space biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) academic.oup.com/bioinformatics…

A remaining hurdle for long-read sequencing is scalability and cost. Here, we developed a single flowcell ONT protocol + push-button pipeline that generates state-of-the-art small and structural variant calls and scales to 1000s of genomes: biorxiv.org/content/10.110…

Seq-InSite: sequence supersedes structure for protein interaction site prediction biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Alex's paper on isONform is now out and will be presented at the iRNA COSI at #ISMB23. Come talk to him :)

Recent alignment methods aim to reduce reference bias, where reads with non-ref alleles fail to align correctly. However, there's a lack of methods for analyzing reference bias. Here we present biastools, which measures and categorizes reference bias. 1/ biorxiv.org/content/10.110…

Mikaël Salson Mikаël Sаlson obtained his HDR yesterday, with a defense entitled Méthodes sans alignement et indexation pour l'analyse de données nucléiques massive (alignment free methods for massive nucleic sequences analysis).

New preprint by Léa Vandamme, Bastien Cazaux and Antoine Limasset

So happy to see this out today - our ultra-fast genome browser GW v1.0 #Genomics 🚀 biorxiv.org/content/10.110…

Our study on methods to detect subgenomic RNAs (sgRNA) is now out. This is work from Thomas Baudeau (from Camille Marchet @[email protected] and Mikаël Sаlson Mikaël Salson's groups), who visited my group last summer. doi.org/10.1093/nar/gk… 1/5

Lilian Marchand, student in Bonsai, will defend his PhD this afternoon, on methods for precise gene-level RNA isoform reconstruction with long reads (Méthodes pour la reconstruction du répertoire des transcrits d’un gène à partir de données RNA-seq de 3ème génération)

The first many-analysts study in ecology is finally published! 🥳🙌 300+ coauthors and 5+ years, this was a massive effort by Elliot Gould Dr Hannah Fraser Tim Parker and co. Open access 👉 bmcbiol.biomedcentral.com/articles/10.11…