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    17 repositories

    • bcalm

      Public
      compacted de Bruijn graph construction in low memory
      bioinformaticsgraphdebruijn
      bioinformaticsgraphdebruijnunitigs
      Python
      •
      MIT License
      •21•100•17•1•Updated Nov 4, 2025Nov 4, 2025

    • gatb-core

      Public
      Core library of the Genome Analysis Toolbox with de-Bruijn graph
      bioinformaticsgenomicsde-bruijn-graphs
      bioinformaticsgenomicsde-bruijn-graphsgatb
      C++
      •29•66•11•1•Updated Feb 1, 2025Feb 1, 2025

    • minia

      Public
      Minia is a short-read assembler based on a de Bruijn graph
      C++
      •
      GNU Affero General Public License v3.0
      •14•78•1•0•Updated Dec 27, 2024Dec 27, 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.
      Python
      •
      GNU Affero General Public License v3.0
      •20•40•3•0•Updated Jun 29, 2023Jun 29, 2023

    • short_read_connector

      Public
      Short Read Connector (SRC)
      C++
      •
      GNU Affero General Public License v3.0
      •5•9•4•0•Updated Feb 2, 2023Feb 2, 2023

    • gatb-minia-pipeline

      Public
      GATB Minia assembly pipeline
      Perl
      •7•32•6•0•Updated Feb 2, 2023Feb 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.
      bioinformaticsgenomicsgatb
      bioinformaticsgenomicsgatbdebruijn-graphstructural-variants
      C++
      •
      GNU Affero General Public License v3.0
      •12•37•0•1•Updated Apr 20, 2022Apr 20, 2022

    • dsk

      Public
      k-mer counting software
      Shell
      •
      GNU Affero General Public License v3.0
      •9•40•5•0•Updated Feb 8, 2022Feb 8, 2022

    • simka

      Public
      Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
      C++
      •
      GNU Affero General Public License v3.0
      •10•51•17•0•Updated Feb 8, 2022Feb 8, 2022

    • github-release-api

      Public
      A script to facilitate the use of Github Release API v3
      Shell
      •
      Apache License 2.0
      •7•0•0•0•Updated Jul 17, 2019Jul 17, 2019

    • leon

      Public
      Leon - FASTA and FASTQ read compressor
      Shell
      •
      GNU Affero General Public License v3.0
      •4•8•7•0•Updated Nov 7, 2018Nov 7, 2018

    • gatb-core-tuto

      Public
      This project hosts the source code of the GATB-Core Programming Online Tutorial.
      JavaScript
      •0•1•1•0•Updated Apr 11, 2018Apr 11, 2018

    • tigops

      Public
      Manipulation of unitigs and contigs
      C++
      •0•2•0•0•Updated Feb 16, 2018Feb 16, 2018

    • pyGATB

      Public
      Python3 wrapper for GATB-Core.
      Python
      •
      GNU Affero General Public License v3.0
      •3•10•1•0•Updated Dec 16, 2017Dec 16, 2017

    • gatb-tools-machine

      Public
      Build a single Docker image containing all GATB-Tools ready to be used. This is an official repository, not a mirror.
      Shell
      •0•2•0•0•Updated Nov 9, 2017Nov 9, 2017

    • bloocoo

      Public
      Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint.
      C++
      •
      GNU Affero General Public License v3.0
      •3•12•0•0•Updated May 22, 2017May 22, 2017

    • TakeABreak

      Public
      TakeABreak detects inversion breakpoints in read datasets without a reference genome
      C++
      •
      GNU Affero General Public License v3.0
      •2•3•0•0•Updated Sep 9, 2016Sep 9, 2016
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