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    • C
      117100Updated Jul 19, 2016Jul 19, 2016
    • vcflib

      Public
      a simple C++ library for parsing and manipulating VCF files
      C++
      MIT License
      221000Updated Jun 24, 2016Jun 24, 2016
    • vt

      Public
      A tool set for short variant discovery in genetic sequence data.
      C
      MIT License
      37000Updated Nov 3, 2015Nov 3, 2015
    • freebayes

      Public
      Bayesian haplotype-based polymorphism discovery and genotyping.
      C++
      MIT License
      264100Updated Aug 30, 2015Aug 30, 2015
    • wham

      Public
      All-things-BAM
      C++
      Other
      25000Updated Apr 21, 2015Apr 21, 2015
    • samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
      C++
      MIT License
      30000Updated Dec 23, 2014Dec 23, 2014
    • RUFUS

      Public
      RUFUS k-mer based genomic variant detection
      C++
      13100Updated Dec 7, 2014Dec 7, 2014
    • gemini

      Public
      a lightweight db framework for disease and population genetics.
      Python
      MIT License
      119000Updated Nov 17, 2014Nov 17, 2014
    • bedtools2

      Public
      A powerful toolset for genome arithmetic.
      C++
      GNU General Public License v2.0
      287000Updated Nov 14, 2014Nov 14, 2014
    • samtools

      Public
      Tools (written in C using htslib) for manipulating next-generation sequencing data
      C
      Other
      582000Updated Nov 11, 2014Nov 11, 2014
    • htslib

      Public
      C library for high-throughput sequencing data formats
      C
      Other
      443000Updated Nov 10, 2014Nov 10, 2014
    • Library for handling tool and pipeline configuration files
      Python
      1000Updated Oct 28, 2014Oct 28, 2014
    • lumpy-sv

      Public
      lumpy: a general probabilistic framework for structural variant discovery
      C
      MIT License
      119000Updated Oct 3, 2014Oct 3, 2014
    • glfFlex

      Public
      C++
      GNU General Public License v3.0
      1000Updated Sep 24, 2014Sep 24, 2014
    • pindel

      Public
      Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
      SystemVerilog
      GNU General Public License v3.0
      90000Updated Aug 27, 2014Aug 27, 2014
    • bwa

      Public
      Burrow-Wheeler Aligner
      C
      GNU General Public License v3.0
      554000Updated Jun 4, 2014Jun 4, 2014
    • Tangram

      Public
      Fast Structural Variation Detection Toolbox
      C++
      MIT License
      6000Updated Jun 4, 2014Jun 4, 2014
    • mutatrix

      Public
      genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms
      C++
      MIT License
      5000Updated May 23, 2014May 23, 2014
    • C++
      14000Updated May 22, 2014May 22, 2014
    • Useful set of classes for creating statistical genetic programs.
      C++
      29000Updated Apr 8, 2014Apr 8, 2014
    • bamUtil

      Public
      C++
      30000Updated Apr 8, 2014Apr 8, 2014
    • MOSAIK

      Public
      reference-guided aligner for next-generation sequencing technologies
      C++
      19000Updated Mar 27, 2014Mar 27, 2014
    • Jellyfish

      Public
      A fast multi-threaded k-mer counter
      C++
      GNU General Public License v3.0
      137000Updated Feb 3, 2014Feb 3, 2014
    • qplot

      Public
      qplot
      C++
      3000Updated Sep 23, 2013Sep 23, 2013
    • Validate FastQ Files
      C++
      10000Updated Nov 13, 2012Nov 13, 2012
    • bamaddrg

      Public
      adds sample names and read-group (RG) tags to BAM alignments
      C++
      13000Updated May 26, 2012May 26, 2012
    • tabix

      Public
      C
      40000Updated Mar 30, 2012Mar 30, 2012
    • bamtools

      Public
      C++ API & command-line toolkit for working with BAM data
      C++
      MIT License
      154100Updated Mar 9, 2012Mar 9, 2012