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    36 repositories

    • BBMap

      Public archive
      (Not Offical) BBMap short read aligner, and other bioinformatic tools.
      Java
      •
      Other
      •111•238•28•1•Updated Feb 11, 2021Feb 11, 2021

    • atropos

      Public
      An NGS read trimming tool that is specific, sensitive, and speedy. (production)
      Python
      •
      Other
      •15•0•0•0•Updated Dec 7, 2020Dec 7, 2020

    • GCE

      Public
      GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size ,genomic repeat content and the heterozygsis rate of the sequencing sample.
      Perl
      •
      GNU General Public License v3.0
      •2•3•0•0•Updated Feb 26, 2020Feb 26, 2020

    • BSVF

      Public
      Bisulfite Sequencing Virus integration Finder
      bisulfitevirus-integration
      C
      •
      GNU Lesser General Public License v3.0
      •5•3•0•0•Updated Nov 29, 2019Nov 29, 2019

    • samtools

      Public
      Tools (written in C using htslib) for manipulating next-generation sequencing data
      C
      •
      Other
      •598•1•0•0•Updated Sep 11, 2018Sep 11, 2018

    • bcftools

      Public
      This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
      C
      •
      Other
      •250•0•0•0•Updated Aug 15, 2018Aug 15, 2018

    • gclib

      Public
      GCLib - Genomic C(++) library of reusable code for bioinformatics projects
      C++
      •
      Other
      •13•0•0•0•Updated Jul 19, 2018Jul 19, 2018

    • csvtk

      Public
      A cross-platform, efficient, practical and pretty CSV/TSV toolkit in Golang
      Go
      •
      MIT License
      •94•0•0•0•Updated Dec 19, 2017Dec 19, 2017

    • fastp

      Public
      A Fast and All-in-one Preprocessor for FastQ files
      C
      •
      MIT License
      •348•0•0•0•Updated Nov 9, 2017Nov 9, 2017

    • kallisto

      Public
      Near-optimal RNA-Seq quantification
      C++
      •
      Other
      •175•0•0•0•Updated Jul 15, 2017Jul 15, 2017

    • treebest

      Public
      TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
      C
      •
      GNU General Public License v2.0
      •12•0•0•0•Updated Apr 10, 2017Apr 10, 2017

    • biscuit

      Public
      BISuilfite-seq CUI Toolkit
      C
      •24•0•0•0•Updated Mar 11, 2017Mar 11, 2017

    • biomake

      Public
      GNU-Make-like utility for managing builds and complex workflows
      Prolog
      •
      BSD 3-Clause "New" or "Revised" License
      •9•0•0•0•Updated Dec 18, 2016Dec 18, 2016

    • historian

      Public
      Reconstruction of phylogenetic insertion-deletion histories
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Dec 15, 2016Dec 15, 2016

    • tiptop

      Public
      Tiptop is a performance monitoring tool for Linux. It provides a dynamic real-time view of the tasks running in the system. tiptop is very similar to the top utility, but most of the information displayed comes from hardware counters.
      C
      •16•0•0•0•Updated Aug 17, 2016Aug 17, 2016

    • diamond

      Public
      Accelerated BLAST compatible local sequence aligner.
      C++
      •181•0•0•0•Updated Jul 30, 2016Jul 30, 2016

    • bamsurgeon

      Public
      tools for adding mutations to existing .bam files, used for testing mutation callers
      Python
      •
      MIT License
      •85•0•0•0•Updated Jul 28, 2016Jul 28, 2016

    • cdhit

      Public
      Automatically exported from code.google.com/p/cdhit
      C++
      •
      GNU General Public License v2.0
      •133•0•0•0•Updated Jul 12, 2016Jul 12, 2016

    • lobstr-code

      Public
      lobSTR: a short tandem repeat profiler for next generation sequencing data
      C++
      •
      GNU General Public License v3.0
      •16•0•0•0•Updated Jul 1, 2016Jul 1, 2016

    • pyensembl

      Public
      Python interface to ensembl reference genome metadata (exons, transcripts, etc...)
      Python
      •
      Apache License 2.0
      •70•0•0•0•Updated Jun 30, 2016Jun 30, 2016

    • pandaseq

      Public
      PAired-eND Assembler for DNA sequences
      C
      •
      GNU General Public License v3.0
      •25•0•0•0•Updated Jun 29, 2016Jun 29, 2016

    • emboss

      Public
      Unofficial mirror of the EMBOSS source
      C
      •
      GNU General Public License v2.0
      •4•0•0•0•Updated Jun 9, 2016Jun 9, 2016

    • phase

      Public
      Code and tests for the phase software
      C++
      •
      Other
      •7•0•0•0•Updated Mar 2, 2016Mar 2, 2016

    • MITObim

      Public
      MITObim - mitochondrial baiting and iterative mapping
      Perl
      •
      MIT License
      •34•0•0•0•Updated Feb 17, 2016Feb 17, 2016

    • canu

      Public
      A single molecule sequence assembler for genomes large and small
      C
      •179•0•0•0•Updated Jan 27, 2016Jan 27, 2016

    • blobtools

      Public
      Application for the visualisation of draft genome assemblies and general QC
      Python
      •47•1•0•0•Updated Jan 12, 2016Jan 12, 2016

    • Complete-Striped-Smith-Waterman-Library

      Public
      C
      •119•0•0•0•Updated Dec 19, 2015Dec 19, 2015

    • blobology

      Public
      Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step
      Perl
      •
      MIT License
      •16•0•0•0•Updated Dec 16, 2015Dec 16, 2015

    • symap

      Public
      Automatically exported from code.google.com/p/symap
      Java
      •0•1•0•0•Updated Oct 27, 2015Oct 27, 2015

    • MACSE

      Public
      Investigation of methods of multiple alignment of the nucleotide sequences in accordance with the reading frame and a stop codon
      C
      •2•0•0•0•Updated Oct 16, 2015Oct 16, 2015