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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 1.9k 617

  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 374

Repositories

Showing 10 of 1416 repositories
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 194 BSD-3-Clause 75 89 34 Updated Nov 3, 2025
  • dig-ldsc-methods Public

    LDSC Methods

    broadinstitute/dig-ldsc-methods’s past year of commit activity
    Python 0 0 0 0 Updated Nov 3, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 216 BSD-3-Clause 111 6 9 Updated Nov 3, 2025
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 150 BSD-3-Clause 25 95 (2 issues need help) 25 Updated Nov 3, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 195 AGPL-3.0 90 53 6 Updated Nov 3, 2025
  • seqr-loading-pipelines Public

    hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

    broadinstitute/seqr-loading-pipelines’s past year of commit activity
    Python 23 MIT 22 20 9 Updated Nov 3, 2025
  • broad-nnfc-hiPSC-to-EC Public
    broadinstitute/broad-nnfc-hiPSC-to-EC’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 3, 2025
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    broadinstitute/dig-aggregator-methods’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 8 Updated Nov 3, 2025
  • cromwell Public

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

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,038 BSD-3-Clause 374 757 55 Updated Nov 3, 2025
  • beehive Public

    Beehive is a web UI for interacting with Sherlock, DSP DevOps's deployment source-of-truth service

    broadinstitute/beehive’s past year of commit activity
    TypeScript 3 BSD-3-Clause 1 0 5 Updated Nov 3, 2025
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