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    42 repositories

    • gkno.github.com

      Public
      JavaScript
      •1•2•3•0•Updated Nov 11, 2017Nov 11, 2017

    • gkno_launcher

      Public
      The gkno launcher for executing tools or pipelines
      Python
      •
      MIT License
      •7•32•23•0•Updated Jan 17, 2017Jan 17, 2017

    • resources-homo_sapiens_grch38

      Public
      Human genome reference build GRCh38/hg38
      0•0•0•0•Updated Sep 28, 2016Sep 28, 2016

    • resources-homo_sapiens_grch37

      Public
      Human genome reference build GRCh37/hg19
      0•0•0•0•Updated Sep 28, 2016Sep 28, 2016

    • Complete-striped-Smith-Waterman-library

      Public
      C
      •113•1•0•0•Updated Jul 19, 2016Jul 19, 2016

    • vcflib

      Public
      a simple C++ library for parsing and manipulating VCF files
      C++
      •
      MIT License
      •221•0•0•0•Updated Jun 24, 2016Jun 24, 2016

    • snpEff

      Public
      Mirror of snpEff variant annotation and effect prediction tool.
      Perl
      •
      GNU Lesser General Public License v3.0
      •1•0•0•0•Updated Nov 24, 2015Nov 24, 2015

    • resources-tutorial

      Public
      gkno resources for use in tutorials
      0•0•0•0•Updated Nov 12, 2015Nov 12, 2015

    • vt

      Public
      A tool set for short variant discovery in genetic sequence data.
      C
      •
      MIT License
      •38•0•0•0•Updated Nov 3, 2015Nov 3, 2015

    • freebayes

      Public
      Bayesian haplotype-based polymorphism discovery and genotyping.
      C++
      •
      MIT License
      •264•1•0•0•Updated Aug 30, 2015Aug 30, 2015

    • resources-homo_sapiens

      Public
      gkno resources for Homo sapiens
      0•0•0•0•Updated Jun 5, 2015Jun 5, 2015

    • genomicRegions

      Public
      Scripts for generating genomic regions for use with other tools.
      Shell
      •0•1•0•0•Updated Apr 27, 2015Apr 27, 2015

    • wham

      Public
      All-things-BAM
      C++
      •
      Other
      •25•0•0•0•Updated Apr 21, 2015Apr 21, 2015

    • samblaster

      Public
      samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
      C++
      •
      MIT License
      •30•0•0•0•Updated Dec 23, 2014Dec 23, 2014

    • RUFUS

      Public
      RUFUS k-mer based genomic variant detection
      C++
      •13•1•0•0•Updated Dec 7, 2014Dec 7, 2014

    • gemini

      Public
      a lightweight db framework for disease and population genetics.
      Python
      •
      MIT License
      •120•0•0•0•Updated Nov 17, 2014Nov 17, 2014

    • bedtools2

      Public
      A powerful toolset for genome arithmetic.
      C++
      •
      GNU General Public License v2.0
      •287•0•0•0•Updated Nov 14, 2014Nov 14, 2014

    • blast

      Public
      Helper repo for fetching NCBI BLAST binaries (http://blast.ncbi.nlm.nih.gov/Blast.cgi)
      0•0•0•0•Updated Nov 11, 2014Nov 11, 2014

    • samtools

      Public
      Tools (written in C using htslib) for manipulating next-generation sequencing data
      C
      •
      Other
      •579•0•0•0•Updated Nov 11, 2014Nov 11, 2014

    • htslib

      Public
      C library for high-throughput sequencing data formats
      C
      •
      Other
      •446•0•0•0•Updated Nov 10, 2014Nov 10, 2014

    • configurationClass

      Public
      Library for handling tool and pipeline configuration files
      Python
      •1•0•0•0•Updated Oct 28, 2014Oct 28, 2014

    • parseSequenceIndex

      Public
      Parse a 1000G sequence index and produce files for use with gkno
      Shell
      •
      MIT License
      •0•0•0•0•Updated Oct 12, 2014Oct 12, 2014

    • lumpy-sv

      Public
      lumpy: a general probabilistic framework for structural variant discovery
      C
      •
      MIT License
      •118•0•0•0•Updated Oct 3, 2014Oct 3, 2014

    • glfFlex

      Public
      C++
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated 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
      •89•0•0•0•Updated Aug 27, 2014Aug 27, 2014

    • genomeStrip

      Public
      Mirror of Genome STRiP from the Broad Institute
      0•0•0•0•Updated Jun 19, 2014Jun 19, 2014

    • bwa

      Public
      Burrow-Wheeler Aligner
      C
      •
      GNU General Public License v3.0
      •555•0•0•0•Updated Jun 4, 2014Jun 4, 2014

    • Tangram

      Public
      Fast Structural Variation Detection Toolbox
      C++
      •
      MIT License
      •6•0•0•0•Updated Jun 4, 2014Jun 4, 2014

    • scripts

      Public
      A set of scripts available within gkno
      MIT License
      •0•0•0•0•Updated Jun 3, 2014Jun 3, 2014

    • mutatrix

      Public
      genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms
      C++
      •
      MIT License
      •5•0•0•0•Updated May 23, 2014May 23, 2014