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

!! Still under development, not yet public !!

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 !!

GraWas. GWAS using pangenome graph

!! Still under development, not yet public !!

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