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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 623

  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 382

  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 377

Repositories

Showing 10 of 1432 repositories
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader’s past year of commit activity
    Jupyter Notebook 3 BSD-3-Clause 0 7 (2 issues need help) 2 Updated Dec 27, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 70 30 21 17 Updated Dec 27, 2025
  • MicroSplit-reproducibility Public Forked from CAREamics/MicroSplit-reproducibility

    Notebooks, scripts and utilities to reproduce MicroSplit

    broadinstitute/MicroSplit-reproducibility’s past year of commit activity
    Python 0 BSD-3-Clause 5 0 0 Updated Dec 26, 2025
  • Drop-seq-wdl Public
    broadinstitute/Drop-seq-wdl’s past year of commit activity
    WDL 0 MIT 0 1 0 Updated Dec 26, 2025
  • viral-references Public

    Reference tables for viral genomics

    broadinstitute/viral-references’s past year of commit activity
    5 BSD-2-Clause 2 0 0 Updated Dec 26, 2025
  • multiVIB Public

    A comprehensive framework for integration of single-cell omics data with probabilistic contrastive learning

    broadinstitute/multiVIB’s past year of commit activity
    Python 0 BSD-3-Clause 0 1 1 Updated Dec 26, 2025
  • Drop-seq Public

    Java tools for analyzing Drop-seq data

    broadinstitute/Drop-seq’s past year of commit activity
    Jupyter Notebook 131 MIT 35 11 0 Updated Dec 26, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 197 AGPL-3.0 92 51 7 Updated Dec 26, 2025
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 159 GPL-3.0 29 32 (1 issue needs help) 26 Updated Dec 25, 2025
  • poolq Public

    The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens

    broadinstitute/poolq’s past year of commit activity
    Scala 5 1 8 (1 issue needs help) 1 Updated Dec 25, 2025
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