Francois Sabot
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francoissabot.bsky.social
Francois Sabot
@francoissabot.bsky.social
400 followers 510 following 650 posts
Scientist, biologist, #evolution and #pangenomics, #bioinformatics, #AI and #OpenScience @ird_fr - and a little bit a #geek too
mastodon: @[email protected]
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Reposted by Francois Sabot
framasoft.org
La complexité de l'affaire rend aujourd'hui extrêmement difficile de lancer un service « Framamail », bien que nous savons toute l'importance de l'adresse e-mail lorsqu'il s'agit de se dégoogliser.

(Désolé, ami·es corses)
Carte style « Asterix » de la campagne Dégooglisons 2016, avec Gmail sur la corse
November 27, 2025 at 7:17 AM
francoissabot.bsky.social
To obtain a clear, non-biased view of #biodiversity, a #pangenome approach is mandatory...
November 25, 2025 at 8:34 AM
Reposted by Francois Sabot
bouletcorp.bsky.social
Un classique parmi les classique: Duty calls, par @xkcd.com
Un personnage est assis à son ordinateur. Une voix off demande: "Tu viens au lit ?", il répond: "Je ne peux pas, c'est important", la voix continue: "Quoi ?", et le personnage: "Quelqu'un a TORT sur Internet".
November 15, 2025 at 5:27 PM
francoissabot.bsky.social
Animals are just a few part... from the same location
Visualizing biomass on earth, not only animals but all kingdoms. Mostly plants, then bacteria, fungi, archae, protists, animals, then viruses. Humans are less than 0.01% of the total biomass...
November 12, 2025 at 9:34 AM
francoissabot.bsky.social
See you on Thursday !
November 4, 2025 at 2:13 PM
francoissabot.bsky.social
Have fun with it!

forge.ird.fr/diade/dynadi...
DIADE / dynadiv / GrAnnoT · GitLab
GitLab Community Edition
forge.ird.fr
October 30, 2025 at 3:46 PM
francoissabot.bsky.social
Nina compared it to state-of-the-art tools for genome-to-genome transfer (LiftOff), genome-to-graph (VG and ODGI), and GrAnnoT is more conservative and fast, and is the only tool able to go efficiently from genome-to-graph AND from graph-to-genome!
Genome to genome transfer comparison. GrAnnoT and Liftoff run time for 1-12 transfers were measured using the command /usr/bin/time. Liftoff was run both in GFF and DB mode. GrAnnoT values are presented including or not the graph building time.
October 30, 2025 at 3:46 PM
francoissabot.bsky.social
Basically, it converts/transfers coordinates from any embedded genome in the graph to the graph, and from the graph to any other embedded genome! It can transfer with a certain level (user defined) of identity/length, and provide alignments between source and target.
GrAnnoT overview. Step 1: the position of the feature is projected from the source genome to the graph using the positions of the nodes on the source genome. Step 2: the position of the feature is projected from the graph to the target genome (a). The first and last nodes from the feature that are on the target genome (the blue ones) are the ends of the feature in this genome, and everything in between is considered as part of the feature. The differences between the two genomes in this region in terms of path in the graph mirror the differences between the two versions of the feature. If these differences are too important and the transfer does not reach the coverage and/or sequence identity thresholds, the annotation is not transferred (b).
October 30, 2025 at 3:46 PM