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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 1415 repositories
  • 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 Oct 29, 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 2 22 2 Updated Oct 29, 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 7 Updated Oct 29, 2025
  • colab-repeat-finder Public

    A tool that finds perfect and nearly-perfect repeats

    broadinstitute/colab-repeat-finder’s past year of commit activity
    Python 2 MIT 0 1 0 Updated Oct 29, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,864 617 1,270 (8 issues need help) 146 Updated Oct 28, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 6 Updated Oct 28, 2025
  • dig-portal-ai Public Forked from yakaboskic/portal-ai

    Framework for applying LLMs to A2F Knowledge Portals

    broadinstitute/dig-portal-ai’s past year of commit activity
    Python 0 Apache-2.0 1 0 10 Updated Oct 28, 2025
  • 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 1 0 8 Updated Oct 28, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 18 Updated Oct 28, 2025
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser’s past year of commit activity
    TypeScript 85 MIT 49 165 (3 issues need help) 8 Updated Oct 28, 2025
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