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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 1.8k 605

  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 378

  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 371

Repositories

Showing 10 of 1398 repositories
  • 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 Jul 18, 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 20 25 3 Updated Jul 18, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 213 BSD-3-Clause 107 5 7 Updated Jul 18, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 190 AGPL-3.0 90 54 6 Updated Jul 18, 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 2 BSD-3-Clause 1 0 10 Updated Jul 18, 2025
  • str-analysis Public

    Scripts and utilities related to analyzing short tandem repeats (STRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 38 MIT 9 0 0 Updated Jul 18, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 190 BSD-3-Clause 75 83 28 Updated Jul 18, 2025
  • lrma-aou1-panel-creation Public

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.

    broadinstitute/lrma-aou1-panel-creation’s past year of commit activity
    WDL 1 1 22 2 Updated Jul 18, 2025
  • dsp-appsec-infrastructure-apps Public

    This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

    broadinstitute/dsp-appsec-infrastructure-apps’s past year of commit activity
    Python 7 BSD-3-Clause 2 0 8 Updated Jul 17, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 12 0 1 39 Updated Jul 17, 2025
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