Francois Sabot

Ravie d’avoir signé hier, un accord-cadre entre l’ @ird-fr.bsky.social & le CAMES
3 axes majeurs : science ouverte, formation et innovation

Une étape importante afin de renforcer nos collaborations institutionnelle, académique et scientifique !🌍

Couverture du guide pour le partage des données liées aux publications scientifiques et annonce de la mise à jour 2025

Mise à jour du guide « Partager les données liées aux publications scientifiques – Guide pour les chercheurs » du comité pour la #scienceouverte : www.ouvrirlascience.fr/partager-les...
#donneesrecherche #entrepotdedonnées

YouTube video by SIB - Swiss Institute of Bioinformatics Tout commence par un point | Ce que la bioinformatique apporte à la science et à la société

À quoi sert la #bioinformatique?

🔴 @sib.swiss nous organisons les données des sciences de la vie, les conservons dans des bases de données et les transformons en connaissances

Découvrez la vidéo ⏩ www.youtube.com/watch?v=BG-h...

Done et lu dans les 15 derniers jours. Très bien écrit et une vision très humaniste in fine de la Mort

© Inria / Photo B. Fourrier

© Inria / Photo B. Fourrier

© Inria / Photo B. Fourrier

Ravie d'avoir signé hier avec Bruno Sportisse le renouvellement du partenariat entre l'INRIA et @ird-fr.bsky.social

Pour une science des données & un numérique frugal, éthique, soutien à l'ESR et qui éclaire les décisions publiques.

Ensemble pour un numérique au service des transitions durables🌿

😁 The EAGS2026 (International Environmental and Agronomical Genomics symposium) program is finally online HERE: eags2026.sciencesconf.org/resource/pag...
⏱️ Registration closes on 14 January!

PCI Statistics and Machine Learning Peer Community in Statistics and Machine Learning

PCI Statistics and Machine Learning (@pcistatml.bsky.social) is now open for submissions!!
statml.peercommunityin.org
For an updated list of all the thematic PCIs, visit peercommunityin.org/current-pcis/

IMO it’s weird and probably irresponsible to teach bioinformatics without some nod to the group dynamics that shaped (otherwise inexplicable) things like the GFF file format or the Gene Ontology. Not to mention why tools back then had names like BLAST and FASTA,but now are named after cuddly animals

Connecting Swiss bioinformatics to the EU - Swisscore Swiss bioinformatics excellence strengthens EU research, from cancer data platforms to genomic tools for biodiversity and conservation.

Connecting Swiss bioinformatics to the EU www.swisscore.org/connecting-s... a briefing from @swissmissioneu.bsky.social highlighting @sib.swiss participation in Horizon Europe projects @biogeneurope.bsky.social & UNCAN-Connect

L’« effet Lazare », ou quand certains êtres vivants ressurgissent après des millions d’années L’« effet Lazare » désigne un phénomène bien plus fréquent qu’on ne le pense : la réapparition de certaines espèces, genres ou familles du vivant que l’on croyait éteintes.

L’« effet Lazare », ou quand certains êtres vivants ressurgissent après des millions d’années

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph Marthe, Nina1  ; Zytnicki, Matthias2 ; Sabot, François1 1 DIADE unit, UM, Cirad, IRD, Montpellier, France 2 MIAT, INRAE, Auzeville-Tolosane, France

Now published in Peer Community Journal, #animalscience section: GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph

Does obligate asexuality necessarily lead to genomic decay? We found that ancient asexual lineages of oribatid mites have static genomes, frozen in time, whereas genomes of sexual lineages seem to be expanding.

En post apo y'a plus sympa comme Metro

Pas le plus fan des livres...

The GraSuite Logo a suite and a tie showing a graph, with a double strand DNA symbolized on the right

In conclusion, GraTools is a powerful too for a one-tool manipulation of GFA pangenome variation graphs!

It is a member of the GraSuite, feel free to discover !

forge.ird.fr/diade/GraSuite

Venn diagram representing the indica and japonica subspecies specific nodes in the Asian Rice graph from Marthe et al, 2025, computed using specific groups samples. For each subspecies (purple for the indica, and orange for the japonica), we indicates the sum in bp of the total nodes (specific or shared).

You can also extract nodes and paths shared ONLY by a subset of embedded individuals, to chek differences between groups for instance

Bandage representation of the Sub1 locus in Asian rice graph from [32].The 3 genes of the locus, namely Sub1C, Sub 1B and Sub1A are depicted in yellow, green and red, respectively on the graph structure

Subgraph extraction, based on these coordinates (from your favorite locus in your favorite sample, for instance), can be then put into Bandage

Overview of GraTools. The central Gratools class coordinates the interactions with three core classes: GFA, GratoolsBam, and SubGraph. The functionalities and commands are organized into four categories: GFA indexing (index), content information (stats, list samples, list chr), data extraction (extract sub graph, get fasta), and content analysis (core dispensable ratio, depth nodes stat, specific groups sample, get segments by depth). The GFA files serve as input, and outputs are provided in BED, BAM, FASTA, GFA and CSV formats, enabling a comprehensive analysis of pangenome variation graphs.

It is structured around a few key classes and features that interact, after converting the graph in BED+ BAM. It allows to interrogate it based on genomic coordinates from *ANY* embedded genome

Screen shot of the readthedocs page saying " GraTools offered a set of commands for analyzing and handling pangenome graphs quickly, whatever the model and therefore the size and the complexity of the GFA file. For example, GraTools allows to extract sequences or subgraphs, convert graphs into FASTA sequences, and identify shared and specific nodes across samples. Additionally, it provides essential statistics for chromosomes and samples data. With multi-threading support and flexible logging capabilities, GraTools is an efficient solution for pangenome graph analysis. GraTools has been developed by IRD and CIRAD, as part of a collaboration between the PANEEC/DIADE and PHIM research teams."

This tool, available as a GNU GPLv3 one, is available here gratools.readthedocs.io/en/latest/

It can extract stats, subgraphs, fasta, count specific nodes and identify specific paths, in an easy and visual way

Example of statistics obtained using the stats command on the NewRiceGraph MGC.gfa.gz graph: gratools stats -g NewRiceGraph MGC.gfa.gz A nice tabular format in rendered in the terminal, with path names, number of nodes, size, etc...

We are pleased to release today GraTools, an user firendly tools to manipulate the #pangenome variation #graph in GFA format.

@ird-fr.bsky.social @cirad.bsky.social @inrae-france.bsky.social

GraTools, an user-friendly tool for exploring and manipulating pangenome variation graphs https://www.biorxiv.org/content/10.64898/2025.12.01.691558v1

Framatoolbox La boîte à outils libre et éthique

Vous avez déjà certainement utilisé des services bourrés de pubs pour découper un PDF, convertir une image ou supprimer l'arrière-plan d'une image.

Framatoolbox vous propose une énorme boîte à outils gratuite et sans pub

framatoolbox.org/abc/fr/

Fini les galères de Wine ? L'outil open source WinBoat change la donne pour Windows sous Linux Plus besoin de bricoler les DLL : WinBoat 0.9.0 virtualise Windows via des conteneurs et supporte désormais Podman et les apps UWP. Et c'est open source !

Application open source du mois : WinBoat, l’outil qui enterre les galères de Wine sous Linux goodtech.info/winboat-0-9-...

A book that reads in block sans serif font, "ARTIFICIAL INTELLIGENCE PROJECTS FOR THE COMMODORE 64." The text is red, switching to gold for the words 'Commodore 64'. Cover bottom, a Commodore 64 - a light brown all-in-one microcomputer with dark brown keys - appears. In the center, a gold PCB in the shape of a human head radiates gold wires in the way wires might radiate from a chip, creating the silhouette of a head; in the center and neck of the head-shaped PCB, chips appear.

Computer scientists believe that soon every home will be able to have their own artificial intelligence machine on their own desktops (Source.)

Carte style « Asterix » de la campagne Dégooglisons 2016, avec Gmail sur la corse

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)

"La condition pour qu’une technologie soit un outil d’émancipation est qu’elle demeure sous contrôle démocratique, à défaut de quoi, immanquablement, elle sera une arme de domination"🗣️

Ma réponse à l'annonce de l'omnibus numérique par la Commission européenne : www.liberation.fr/idees-et-deb...

🗓️ Framadate fait peau neuve !

Notre service, sorti en 2011, avait bien besoin de se rafraîchir.
Cette nouvelle version, basée sur un tout nouveau logiciel, propose un nouveau design accessible et adapté aux mobiles ! 📱

Faites un tour des nouveautés sur le Framablog : framablog.org/2025/11/25/f...

A possible pipeline for the uses of a pangenome graph. This pipeline can be roughly divided into three main sections (on the right): build a graph, using it, and adding reads. A first pangenome graph is created, usually with almost complete haplotype as- semblies. Since graph creating methods vary, and may be fraught with errors (unaligned regions, broken paths), assessing the quality of a graph is useful (this can be applied after each subsequent step). Similarly, it is also crucial to be able to visualize the graph, espe- cially on particular loci of interest (can also be done throughout the pipe-line). The graph can be augmented with additional data increasing allele counts, including known con- tig alignment or read mapping. Several augmentation iterations, with different types of data, can be considered. Since most analyses focus on genes and transposable elements, it is usually useful to add an annotation (available on one or several reference genomes), which projected to the graph. This graph, possibly extended with new variants and an- notation, should be then shared with the community, following FAIR practices. Most analyses then focus on graphs with only one species, and the graph can be analyzed in order to find regions of interest. However, dual pangenomics, which studies the joint diversities of two species, can be envisioned. More generally, many species can also be modeled, for instance in the case of meta-genomics. Low coverage sequencing data of individuals can be compared or aligned to the graph in order to produce large genotyp- ing sets enabling population genetics studies (i.e. coalescence, association). Other omics (e.g. RNA-Seq, ChIP-Seq, Hi-C, LC-MS, BS-Seq etc.) data can be added to the graph, and potentially aggregated to multi-omic layers.

With many colleagues, we tried to gather the future prospects and challenges for #Pangenomics and #Pangenome research in agronomy, that can however be adopted more largely

hal.science/hal-05357866/

@ird-fr.bsky.social @inrae-france.bsky.social #FAIR #OpenScience #vizu

To obtain a clear, non-biased view of #biodiversity, a #pangenome approach is mandatory...

Variant Calling in the Goldilocks Zone: How Reference Genome Choice and Read Mapping Stringency Impact Heterozygosity Estimates and Phylogenetic Analyses The increasing numbers of published reference genomes and affordability of whole genome resequencing have enabled multispecies population genomic and phylogenomic studies on non-model organisms, but ....

Analysis of read mapping accuracy and efficiency, missing data, heterozygosity, and inferred phylogenies to evaluate the impact of reference #genome and read-mapping method onlinelibrary.wiley.com/doi/10.1111/...