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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 607

  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 369

Repositories

Showing 10 of 1391 repositories
  • 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 1,023 BSD-3-Clause 369 751 51 Updated Jun 27, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 189 BSD-3-Clause 75 85 28 Updated Jun 27, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 188 AGPL-3.0 90 53 1 Updated Jun 27, 2025
  • SpliceAI-lookup Public

    Website for checking SpliceAI and Pangolin scores:

    broadinstitute/SpliceAI-lookup’s past year of commit activity
    HTML 25 MIT 7 3 0 Updated Jun 27, 2025
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 145 BSD-3-Clause 24 95 (2 issues need help) 26 Updated Jun 27, 2025
  • PromoterAI-lookup Public

    Clone of SpliceAI-lookup as a companion to the PromoterAI paper

    broadinstitute/PromoterAI-lookup’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Jun 27, 2025
  • faris Public

    Server for embeddings of graph nodes

    broadinstitute/faris’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Jun 27, 2025
  • data-registry-api Public
    broadinstitute/data-registry-api’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 1 Updated Jun 27, 2025
  • stp_segmentation_wdl Public
    broadinstitute/stp_segmentation_wdl’s past year of commit activity
    WDL 0 0 0 0 Updated Jun 27, 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 1 Updated Jun 27, 2025
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