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    20 repositories

    • biobuilds

      Public
      Curated collection of open-source bioinformatics tools
      Shell
      •
      Other
      •3•28•2•0•Updated Feb 5, 2019Feb 5, 2019

    • python3statement.github.io

      Public
      CSS
      •
      Other
      •121•0•0•0•Updated Jan 25, 2019Jan 25, 2019

    • cufflinks

      Public
      C++
      •
      Boost Software License 1.0
      •116•0•1•0•Updated Jan 5, 2019Jan 5, 2019

    • docker

      Public
      BioBuilds-related Docker images and utilities
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 27, 2018Dec 27, 2018

    • bwa

      Public
      Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
      C
      •
      GNU General Public License v3.0
      •556•0•0•0•Updated Aug 22, 2018Aug 22, 2018

    • bowtie2

      Public
      A fast and sensitive gapped read aligner
      C++
      •
      GNU General Public License v3.0
      •158•0•0•0•Updated May 2, 2018May 2, 2018

    • bamkit

      Public
      Tools for common BAM file manipulations
      Python
      •
      MIT License
      •6•0•0•0•Updated Nov 9, 2017Nov 9, 2017

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •588•0•0•0•Updated Sep 6, 2017Sep 6, 2017

    • libgtextutils

      Public
      Gordon's Text utils Library
      C++
      •
      GNU Affero General Public License v3.0
      •17•0•0•0•Updated Aug 14, 2017Aug 14, 2017

    • fastx_toolkit

      Public
      FASTA/FASTQ pre-processing programs
      C
      •
      Other
      •60•0•0•0•Updated Aug 14, 2017Aug 14, 2017

    • vcflib

      Public
      a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
      C++
      •
      MIT License
      •221•0•0•0•Updated May 30, 2017May 30, 2017

    • ngs

      Public
      NGS Language Bindings
      C++
      •
      Other
      •52•0•0•0•Updated Nov 17, 2016Nov 17, 2016

    • sra-tools

      Public
      SRA Tools
      Shell
      •
      Other
      •245•0•0•0•Updated Nov 17, 2016Nov 17, 2016

    • oases

      Public
      De novo transcriptome assembler for short reads
      C
      •
      GNU General Public License v3.0
      •9•0•0•0•Updated Nov 1, 2016Nov 1, 2016

    • plink-ng

      Public
      A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).
      C
      •
      GNU General Public License v3.0
      •124•0•0•0•Updated Oct 20, 2016Oct 20, 2016

    • chimerascan

      Public
      Automatically exported from code.google.com/p/chimerascan
      Python
      •
      GNU General Public License v3.0
      •0•0•15•0•Updated Mar 21, 2016Mar 21, 2016

    • bioperl-ext

      Public
      XS-based BioPerl extensions to C libraries (defunct)
      C
      •8•0•0•0•Updated Mar 7, 2016Mar 7, 2016

    • ncbi-vdb

      Public
      ncbi-vdb
      C
      •
      Other
      •38•0•0•0•Updated Feb 16, 2016Feb 16, 2016

    • SOAPdenovo2

      Public
      Next generation sequencing reads de novo assembler.
      C
      •
      GNU General Public License v3.0
      •78•0•0•0•Updated Jul 1, 2015Jul 1, 2015

    • CEGMA_v2

      Public
      The final version 2 release of our software to detect core genes in eukaryotic genomes
      Perl
      •10•0•0•0•Updated Mar 31, 2015Mar 31, 2015