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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 626

  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 1536 repositories
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr's past year of commit activity
    Python 218 AGPL-3.0 97 45 7 Updated Sep 15, 2026
  • via Public

    A new variant interpretation tool for the All of Us Researcher Workbench, leveraging linked genomic and phenotypic data to support clinical classification

    broadinstitute/via's past year of commit activity
    TypeScript 2 0 0 1 Updated Sep 15, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv's past year of commit activity
    Python 207 BSD-3-Clause 82 100 29 Updated Sep 15, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 1,998 626 1,292 (8 issues need help) 157 Updated Sep 15, 2026
  • sparklespray Public

    Easy batch submission of adhoc jobs onto GCP

    broadinstitute/sparklespray's past year of commit activity
    Go 13 4 1 11 Updated Sep 15, 2026
  • regional_missense_constraint Public

    Code to calculate regional missense constraint

    broadinstitute/regional_missense_constraint's past year of commit activity
    Python 13 BSD-3-Clause 2 0 3 Updated Sep 15, 2026
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal's past year of commit activity
    TypeScript 8 BSD-2-Clause 2 1 7 Updated Sep 15, 2026
  • dig-knowledge-graph Public
    broadinstitute/dig-knowledge-graph's past year of commit activity
    Python 0 1 2 0 Updated Sep 15, 2026
  • cds-daintree Public
    broadinstitute/cds-daintree's past year of commit activity
    Python 1 2 0 2 Updated Sep 15, 2026
  • dig-job-server Public
    broadinstitute/dig-job-server's past year of commit activity
    Vue 0 0 0 4 Updated Sep 15, 2026
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