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@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 2k 625

  2. picard picard Public

    A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

    Java 1.1k 385

  3. cromwell cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    Scala 1.1k 381

Repositories

Showing 10 of 1535 repositories
  • genohype Public

    Fast, memory-efficient toolkit for querying Hail tables and VCFs, exporting genomic data, and running distributed GCP jobs.

    broadinstitute/genohype's past year of commit activity
    Rust 4 MIT 0 1 19 Updated Sep 10, 2026
  • gnomad_chets Public

    Phase of compound heterozygotes in gnomAD

    broadinstitute/gnomad_chets's past year of commit activity
    HTML 7 BSD-3-Clause 0 2 2 Updated Sep 10, 2026
  • dig-job-server Public
    broadinstitute/dig-job-server's past year of commit activity
    Vue 0 0 0 4 Updated Sep 10, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 1,996 625 1,292 (8 issues need help) 155 Updated Sep 10, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    WDL 229 BSD-3-Clause 118 13 22 Updated Sep 10, 2026
  • scat-parse Public Forked from typelevel/cats-parse

    A parsing library for Scattaca DNA

    broadinstitute/scat-parse's past year of commit activity
    Scala 0 MIT 55 0 0 Updated Sep 10, 2026
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader's past year of commit activity
    JavaScript 6 BSD-3-Clause 0 9 (1 issue needs help) 4 Updated Sep 10, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr's past year of commit activity
    Python 217 AGPL-3.0 97 43 11 Updated Sep 10, 2026
  • dig-artifact-provenance Public
    broadinstitute/dig-artifact-provenance's past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 10, 2026
  • gnomad-deployments Public

    kustomizations for current gnomad project kubernetes deployments

    broadinstitute/gnomad-deployments's past year of commit activity
    Makefile 1 1 0 4 Updated Sep 10, 2026
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