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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 1.9k 624

  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 382

  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 378

Repositories

Showing 10 of 1452 repositories
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 200 AGPL-3.0 93 45 14 Updated Mar 1, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 201 BSD-3-Clause 76 97 26 Updated Mar 1, 2026
  • bican-mccarroll-manuscript1 Public

    Scripts used to process data for the first McCarroll lab BICAN manuscript

    broadinstitute/bican-mccarroll-manuscript1’s past year of commit activity
    R 0 MIT 0 0 2 Updated Mar 1, 2026
  • collab-sync Public
    broadinstitute/collab-sync’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Mar 1, 2026
  • thurloe Public

    A simple service to store arbitrary key/value pairs

    broadinstitute/thurloe’s past year of commit activity
    Scala 3 BSD-3-Clause 0 0 1 Updated Mar 1, 2026
  • sam Public

    workbench identity and access management

    broadinstitute/sam’s past year of commit activity
    Scala 43 BSD-3-Clause 12 3 10 Updated Mar 1, 2026
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 4 Updated Mar 1, 2026
  • python-cert_manager Public

    Python interface to the Sectigo Certificate Manager REST API

    broadinstitute/python-cert_manager’s past year of commit activity
    Python 42 BSD-3-Clause 22 2 1 Updated Mar 1, 2026
  • dcc_pigean_flask Public

    Flask server for the Pigean method

    broadinstitute/dcc_pigean_flask’s past year of commit activity
    Python 0 0 4 12 Updated Mar 1, 2026
  • TAG-public Public

    Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)

    broadinstitute/TAG-public’s past year of commit activity
    WDL 5 3 1 15 Updated Mar 1, 2026
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