François Sabot

Complete pangenome graph annotation with GrAnnoT and GrAPEx

The paper introduces GrAnnoT and GrAPEx to fully annotate pangenome graphs, integrating annotations from multiple genomes and annotating non-annotated regions, reducing reference bias.

SaVanache: indexing and visualizing pangenome variation graphs

SaVanache provides a visualization tool for exploring pangenome variation graphs, enabling interactive analysis of genetic diversity and structural variations.

Pangenome Graph Node-Phenotype Association shows GWAS-like quality results with only few individuals

GraNPA identifies phenotype-associated genomic regions using pangenome graphs with few individuals, achieving GWAS-like results without population materials or kinship data.

GraTools, an user-friendly tool for exploring and manipulating pangenome variation graphs

GraTools is a command-line tool for manipulating pangenome variation graphs, enabling efficient subgraph extraction, sequence retrieval, and analysis of genomic diversity.

Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and function of outlier chromosomes

The paper presents 28 high-quality genome sequences of Bathycoccus species, revealing structural variations and haplotype diversity, and provides genomic resources to study eukaryotic phytoplankton diversity and evolution.

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph

GrAnnoT transfers annotations to pangenome graphs, improving their utility for genomic analysis across species.

DateBack, an evolving open-access repository of Phoenix archaeobotanical data supporting new perspectives on the history of date palm cultivation

DateBack compiles and standardizes archaeobotanical data on date palms, revealing cultivation timelines and regional disparities in the history of date palm use.

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

This study uses long-read RNA-seq to identify and quantify transposable element transcripts at the copy level in Drosophila germline tissues, revealing differences in their transcriptional landscape between testes and ovaries.

Transposable elements contribute to the evolution of host shift-related genes in cactophilic Drosophila species

This study investigates the role of transposable elements (TEs) in host shift-related genes of cactophilic Drosophila species, finding enrichment of TEs at promoter regions and their contribution to gene expression divergence.

Complete mitochondrial genome and draft chloroplastic genome of Northern Atlantic Haslea ostrearia (Gaillon/Bory) Simonsen, 1974 (Naviculaceae, Bacillariophyceae)

The paper describes the first completed mitochondrial genome and draft chloroplast genome of Haslea ostrearia, providing genetic insights into its structure and phylogenetic relationships.

CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

CulebrONT is a pipeline that streamlines long-read genome assembly by integrating multiple assemblers and providing quality metrics.

TrEMOLO: Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches

TrEMOLO estimates transposable element allele frequencies using long-read sequencing data by combining assembly and mapping approaches, outperforming existing tools in benchmark tests.

Panache: a Web Browser-Based Viewer for Linearized Pangenomes

Panache provides a web-based tool for visualizing linear pangenomes with presence-absence variations and additional tracks.

TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses

Comparison of two African rice species through a new pan-genomic approach on massive data

The paper compares two African rice species using a pan-genomic approach, finding that the cultivated species has a smaller core-genome and dispensable genome compared to the wild species.