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URGI-Anagen

Groupe rassemblant les membres de l'équipe analyse des génomes de l'URGI

  • C

    Caulifinder : a pipeline for automatic detection and annotation of caulimovirid endogenous viral elements in plant genomes

  • C

    In frame of EVENT project, all code to build a docker image for the Caulifinder tool. It allows discovering Caulimoviridae sequences in plant genomes.

  • P

    panREPET is a pipeline detecting shared Transposable Element (TE) insertions among a pangenome. It takes in charge multiple de novo whole-genome assemblies of the same species. It compares TE copies between each pair of genomes then identifies TE copies shared by a group of individuals.

  • P

    panTEannot serially annotates transposable elements from multiple genomes using a common reference library. The annotation is a light version of TEannot from REPET package. These annotations can be used as input for the panREPET tool.

  • REPET-snakemake
  • T

    A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

  • W

    wiki for REPET usage