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@broadinstitute

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 381

  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 1440 repositories
  • 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 Jan 26, 2026
  • 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 23 21 5 Updated Jan 26, 2026
  • bits-appengine Public

    BITS AppEngine Python Package

    broadinstitute/bits-appengine’s past year of commit activity
    Python 0 0 0 2 Updated Jan 26, 2026
  • str-truth-set Public

    Genome-wide tandem repeat (TR) truth set based on the Synthetic Diploid Benchmark [Li et al. 2018]

    broadinstitute/str-truth-set’s past year of commit activity
    Python 8 MIT 0 0 1 Updated Jan 26, 2026
  • TRExplorer Public

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

    broadinstitute/TRExplorer’s past year of commit activity
    HTML 0 MIT 0 2 0 Updated Jan 26, 2026
  • str-analysis Public

    Scripts and utilities for analyzing tandem repeats (TRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 42 MIT 11 0 0 Updated Jan 25, 2026
  • viral-phylo Public

    viral-ngs: phylogenetics, annotation, intrahost variants

    broadinstitute/viral-phylo’s past year of commit activity
    Python 4 0 9 3 Updated Jan 25, 2026
  • haplograph Public
    broadinstitute/haplograph’s past year of commit activity
    WDL 1 MIT 0 0 0 Updated Jan 25, 2026
  • permutect Public

    Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

    broadinstitute/permutect’s past year of commit activity
    Python 8 1 10 2 Updated Jan 25, 2026
  • 2025_varchamp_snakemake Public
    broadinstitute/2025_varchamp_snakemake’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Jan 25, 2026
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