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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 1.8k 615

  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 1k 380

  3. cromwell cromwell Public

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

    Scala 1k 373

Repositories

Showing 10 of 1407 repositories
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 142 27 30 (1 issue needs help) 24 Updated Sep 10, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 193 BSD-3-Clause 77 87 31 Updated Sep 10, 2025
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 2 2 0 Updated Sep 10, 2025
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 68 BSD-3-Clause 27 6 11 Updated Sep 10, 2025
  • ops-terra-utils Public
    broadinstitute/ops-terra-utils’s past year of commit activity
    Python 6 3 0 2 Updated Sep 10, 2025
  • BE3D Public

    BE3D public repository

    broadinstitute/BE3D’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 10, 2025
  • ddp-study-server Public

    Pepper Study Server

    broadinstitute/ddp-study-server’s past year of commit activity
    Java 8 BSD-3-Clause 7 1 2 Updated Sep 10, 2025
  • malaria Public
    broadinstitute/malaria’s past year of commit activity
    R 1 MIT 0 0 0 Updated Sep 10, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 194 AGPL-3.0 90 53 4 Updated Sep 10, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 215 BSD-3-Clause 111 5 7 Updated Sep 10, 2025
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