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Genome Analysis Toolbox with de-Bruijn graph

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  1. bcalm bcalm Public

    compacted de Bruijn graph construction in low memory

    Python 99 20

  2. minia minia Public

    Minia is a short-read assembler based on a de Bruijn graph

    C++ 72 14

  3. gatb-core gatb-core Public

    Core library of the Genome Analysis Toolbox with de-Bruijn graph

    C++ 63 27

  4. simka simka Public

    Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.

    C++ 46 10

  5. dsk dsk Public

    k-mer counting software

    Shell 38 9

  6. DiscoSnp DiscoSnp Public

    DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

    Python 38 20

Repositories

Showing 10 of 17 repositories
  • minia Public

    Minia is a short-read assembler based on a de Bruijn graph

    GATB/minia’s past year of commit activity
    C++ 72 AGPL-3.0 14 1 0 Updated Oct 4, 2024
  • gatb-core Public

    Core library of the Genome Analysis Toolbox with de-Bruijn graph

    GATB/gatb-core’s past year of commit activity
    C++ 63 27 11 1 Updated Oct 4, 2024
  • bcalm Public

    compacted de Bruijn graph construction in low memory

    GATB/bcalm’s past year of commit activity
    Python 99 MIT 20 17 1 Updated Oct 4, 2024
  • DiscoSnp Public

    DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

    GATB/DiscoSnp’s past year of commit activity
    Python 38 AGPL-3.0 20 2 0 Updated Jun 29, 2023
  • short_read_connector Public

    Short Read Connector (SRC)

    GATB/short_read_connector’s past year of commit activity
    C++ 10 AGPL-3.0 5 4 0 Updated Feb 2, 2023
  • gatb-minia-pipeline Public

    GATB Minia assembly pipeline

    GATB/gatb-minia-pipeline’s past year of commit activity
    Perl 29 8 6 0 Updated Feb 2, 2023
  • MindTheGap Public

    MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

    GATB/MindTheGap’s past year of commit activity
    C++ 38 AGPL-3.0 12 0 1 Updated Apr 20, 2022
  • dsk Public

    k-mer counting software

    GATB/dsk’s past year of commit activity
    Shell 38 AGPL-3.0 9 4 0 Updated Feb 8, 2022
  • simka Public

    Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.

    GATB/simka’s past year of commit activity
    C++ 46 AGPL-3.0 10 17 0 Updated Feb 8, 2022
  • github-release-api Public Forked from pgdurand/github-release-api

    A script to facilitate the use of Github Release API v3

    GATB/github-release-api’s past year of commit activity
    Shell 0 Apache-2.0 9 0 0 Updated Jul 17, 2019

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