Alternatives and similar repositories for gemini:

Users that are interested in gemini are comparing it to the libraries listed below

• counsyl / hgvs
  HGVS variant name parsing and generation
  ☆174Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆371Updated last year
• 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…
  ☆122Updated 5 years ago
• konradjk / loftee
  ☆174Updated last year
• konradjk / exac_browser
  Browser for ExAC consortium data
  ☆106Updated 3 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 3 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆310Updated 9 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆194Updated last year
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆314Updated 3 years ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• broadinstitute / mutect
  MuTect -- Accurate and sensitive cancer mutation detection
  ☆96Updated 2 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…
  ☆294Updated 6 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆319Updated last year
• AstraZeneca-NGS / VarDictJava
  VarDict Java port
  ☆133Updated last year
• brentp / bio-playground
  miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
  ☆182Updated 6 years ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆176Updated 11 months ago
• broadinstitute / seqr
  web-based analysis tool for rare disease genomics
  ☆185Updated this week
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆239Updated 5 months ago
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆324Updated this week
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆423Updated 8 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆267Updated last year
• OpenGene / MutScan
  Detect and visualize target mutations by scanning FastQ files directly
  ☆151Updated 3 years ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆496Updated this week
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆322Updated 2 years ago
• ga4gh / ga4gh-server
  Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
  ☆98Updated 7 years ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆196Updated last year
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆150Updated 2 years ago
• macarthur-lab / gene_lists
  List of gene lists for genomic analyses.
  ☆218Updated 2 years ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆392Updated 6 months ago