Sophie Schbath
LightNews LightNews
banner
sophieschbath.bsky.social
Sophie Schbath
@sophieschbath.bsky.social
510 followers 140 following 61 posts
Researcher at INRAE MaIAGE lab #statistics #bioinformatics, scientific head of MIGALE bioinformatics facility, more and more concerned about environmental impacts of our activites
Posts Replies Media Videos
Reposted by Sophie Schbath
sinamajidian.bsky.social
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Figure 1: (A) Anchor-based merging requires a common sequence (red) present in each partition. Multi-MUMs are merged by identifying overlaps between partition-specific matches in the anchor coordinate space, and a uniqueness threshold determines if a MUM is still unique in each partition after truncation. (B) String-based merging enables compu- tation of multi-MUMs between partitions without a common sequence. An example tree (left) is shown, highlighting the use case where partial multi-MUMs specific to internal nodes (starred) can be computed by merging subclade-based partitions up a tree. (right) MUM overlaps are computed by running Mumemto on the MUM sequences, and the uniqueness threshold array ensures overlaps remain unique across the merged dataset. (C) An example Burrows-Wheeler Transform (BWT), matrix (BWM), and Longest Com- mon Prefix (LCP) array, with sequence IDs for each suffix shown (ID). A non-maximal unique match (UM) is shown, and the uniqueness threshold for this match is found us- ing the flanking LCP values. (D) A partial multi-MUM (in blue) is found in all-but-one sequence (excluded in red). Using two anchor sequences (red and orange), all-but-one partial MUMs can be computed using an augmented anchor-based merging method (sec- tion 2.6).
November 6, 2025 at 1:13 AM
Reposted by Sophie Schbath
sinamajidian.bsky.social
Jacqueline Toussaint gave the talk on "Constructing pan-genome gene graphs with hundreds of thousands of bacterial genomes"
The pipeline reveals bacterial variations using PopPUNK to cluster isolates, followed by finding genes and graphing with ggCaller/Panaroo, on the great AlltheBacteria! #GI2025
November 6, 2025 at 1:37 AM
Reposted by Sophie Schbath
sinamajidian.bsky.social
Nicole Brown gave a fantastic talk on Identifying introgressions across pangenomes with Panagram

It uses k-mer conservation to annotate genomic variation across hundreds of genomes, followed by normalization of k-mer profiles to identify introgression events
github.com/kjenike/pana... #GI2025
November 6, 2025 at 2:52 AM
Reposted by Sophie Schbath
ccailleaux.bsky.social
Mais cela n'est pas qu'un constat pessimiste. C'est aussi une clé pour s'en sortir. Notre objectif doit d'abord être de préserver notre capacité à vivre sans les IA. À nous déplacer, apprendre, créer, parler, aimer, vivre ! sans recours imposés aux IA.
November 4, 2025 at 6:14 PM