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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 603

  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 373

  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 362

Repositories

Showing 10 of 1376 repositories
  • 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 29 3 Updated Apr 25, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 187 BSD-3-Clause 75 82 23 Updated Apr 25, 2025
  • ABC-Enhancer-Gene-Prediction Public

    Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

    broadinstitute/ABC-Enhancer-Gene-Prediction’s past year of commit activity
    Python 225 MIT 68 5 0 Updated Apr 25, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 5 Updated Apr 25, 2025
  • idmp-fungal-pipelines Public
    broadinstitute/idmp-fungal-pipelines’s past year of commit activity
    WDL 0 GPL-3.0 0 0 0 Updated Apr 25, 2025
  • tandem-repeat-explorer Public

    An online portal for exploring genome-wide TR catalogs

    broadinstitute/tandem-repeat-explorer’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Apr 25, 2025
  • palantir-workflows Public

    Utility workflows for the DSP hydro.gen team (formerly palantir)

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 24 BSD-3-Clause 9 4 2 Updated Apr 25, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 211 BSD-3-Clause 102 5 11 Updated Apr 25, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,798 603 1,245 (8 issues need help) 136 Updated Apr 25, 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 4 Updated Apr 25, 2025
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