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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 622

  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
    HTML 3 BSD-3-Clause 0 7 (2 issues need help) 2 Updated Dec 25, 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 0 1 0 Updated Dec 25, 2025
  • Drop-seq-wdl Public
    broadinstitute/Drop-seq-wdl’s past year of commit activity
    WDL 0 MIT 0 1 0 Updated Dec 25, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 70 30 21 17 Updated Dec 24, 2025
  • trexplorer-catalog Public

    Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]

    broadinstitute/trexplorer-catalog’s past year of commit activity
    Python 17 MIT 1 0 0 Updated Dec 24, 2025
  • TRExplorer Public

    An online portal for exploring tandem repeats (TRs) genome-wide.

    broadinstitute/TRExplorer’s past year of commit activity
    HTML 0 MIT 0 3 0 Updated Dec 24, 2025
  • str-analysis Public

    Scripts and utilities for analyzing tandem repeats (TRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 42 MIT 10 0 0 Updated Dec 24, 2025
  • str-truth-set-v2 Public
    broadinstitute/str-truth-set-v2’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Dec 24, 2025
  • lrma-aou2-panel-creation Public Forked from broadinstitute/lrma-aou1-panel-creation

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 2 long-reads callset.

    broadinstitute/lrma-aou2-panel-creation’s past year of commit activity
    0 2 0 1 Updated Dec 24, 2025
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 158 GPL-3.0 29 32 (1 issue needs help) 26 Updated Dec 24, 2025
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