Alternatives and similar repositories for gatk-protected

Users that are interested in gatk-protected are comparing it to the libraries listed below

• sequencing / isaac_variant_caller
  This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka
  ☆37Updated 8 years ago
• broadgsa / gatk
  Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…
  ☆299Updated 7 years ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆318Updated 3 years ago
• counsyl / hgvs
  HGVS variant name parsing and generation
  ☆176Updated 2 years ago
• broadinstitute / gatk-protected
  Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
  ☆32Updated 8 years ago
• arq5x / bedtools
  A powerful toolset for genome arithmetic.
  ☆142Updated 4 years ago
• broadinstitute / mutect
  MuTect -- Accurate and sensitive cancer mutation detection
  ☆102Updated 2 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆204Updated 4 years ago
• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 years ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆175Updated 6 years ago
• brentp / bio-playground
  miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
  ☆182Updated 7 years ago
• konradjk / exac_browser
  Browser for ExAC consortium data
  ☆106Updated 3 years ago
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆237Updated 4 years ago
• OpenGene / MutScan
  Detect and visualize target mutations by scanning FastQ files directly
  ☆157Updated 3 years ago
• KHP-Informatics / ngseasy
  Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
  ☆86Updated 8 years ago
• DaehwanKimLab / tophat
  Spliced read mapper for RNA-Seq
  ☆92Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated 2 years ago
• amplab / snap
  Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
  ☆297Updated 4 months ago
• mozack / abra2
  ABRA2
  ☆95Updated 3 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 8 months ago
• jts / sga
  de novo sequence assembler using string graphs
  ☆243Updated 6 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆160Updated 3 years ago
• Illumina / interop
  C++ Library to parse Illumina InterOp files
  ☆80Updated last month
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆75Updated 6 years ago
• macarthur-lab / clinvar
  This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file…
  ☆128Updated 5 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆250Updated 4 months ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆110Updated 5 years ago
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆126Updated 2 years ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆175Updated last year