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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 602

  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 999 372

  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 359

Repositories

Showing 10 of 1349 repositories
  • tensorqtl Public

    Ultrafast GPU-enabled QTL mapper

    broadinstitute/tensorqtl’s past year of commit activity
    Python 170 BSD-3-Clause 53 39 2 Updated Mar 9, 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 216 MIT 66 7 1 Updated Mar 9, 2025
  • palantir-workflows Public

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

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 23 BSD-3-Clause 8 4 3 Updated Mar 9, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 0 0 Updated Mar 9, 2025
  • broad-epi-workflows-collection Public

    This repo contains WDL workflows written by the Epigenomics program.

    broadinstitute/broad-epi-workflows-collection’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 9, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,778 602 1,237 (8 issues need help) 131 Updated Mar 9, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 185 AGPL-3.0 89 49 4 Updated Mar 9, 2025
  • starrynight Public

    Library and tools to process cell painting images

    broadinstitute/starrynight’s past year of commit activity
    Python 2 BSD-3-Clause 0 28 3 Updated Mar 9, 2025
  • 2025_varchamp_snakemake Public
    broadinstitute/2025_varchamp_snakemake’s past year of commit activity
    Python 0 0 0 0 Updated Mar 9, 2025
  • pyqtl Public

    Collection of analysis tools for quantitative trait loci

    broadinstitute/pyqtl’s past year of commit activity
    Python 51 BSD-3-Clause 8 0 2 Updated Mar 8, 2025
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