Software

Next and Third Generation sequencing

  • GATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.
    These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Among them are (the full is available here: https://gatb.inria.fr/software/):

    • de-novo pipelinede-novo assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes
    • DSK: Count K-mer in sequences
    • Leon: COmpress reads
    • Bloocoo: Correct reads
    • BCALM: Construct compacted de Bruijn graphs (unitigs)
    • Minia: Assemble reads
    • Mapsembler2: Targeted assembly
    • DiscoSNP++: Discover SNPs and indels from non-assembled reads without reference genome
    • MindTheGap: Detect insertion variants
    • TakeABreak: Discover inversion from non-assembled data
    • Simka: Comparative metagenomics for large-scale datasets
    • short read connector: Detect similar reads from potentially large read set
  • Non GATB NGS and TGS software:

 

 Protein Structure

  • A_Purva: Contact Map Overlap solver
  • MD-Jeep: Distance Geometry solver
  • CSA: Comparative Structural Alignment

Workflow

  • SLICEE: parallel execution of bioinformatics workflows

Comparative Genomics

  • CASSIS: detection of rearrangement breakpoints

Permanent link to this article: https://team.inria.fr/genscale/software-2/