Representing a pangenome is always easier in a drawing than in reality (© IRD – Eloi Durant)

PUBLICATIONS

An up-to-date list of team members publication is available here

TOOLS, PIPELINES, SOFTWARES                                

Construction, visualisation & manipulation of pangenomes

FrangiPANe. Construction of a pangenome reference using the map-then-assembly approach

Panache. Visualisation of linearized pangenomes

Savanache. Visualisation of structural variations in linearized pangenomes pangenomes

GraSuite. A suite of awesome tools for GFA pangenome graph manipulation and pangenome in general

GraTools. Manipulation of pangenome graphs

GrAnnoT. Annotation transfer tool for pangenome graphs

GraDiv.  Diversity analysis on a pangenome graph

GraDex. indexation of graph for fast query retrieval

!! Still under development, not yet public !!

GraPheus. A pangenome graph simulator

!! Still under development, not yet public !!

GraNPA. GWAS using pangenome graph

Transposable elements

TrEMOLO. Detection of transposable elements using assembly- and mapping-based approaches

LTRclassifier. Classification of LTR retrotransposons in plants

NGS analyses

CulebrONT. Long reads multi-assembler pipeline

TOGGLe. Building workflows and performing NGS analyses

DuplicationDetector. Detection of duplication using NGS data