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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 1.7k 596

  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 991 371

  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 360

Repositories

Showing 10 of 1332 repositories
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,743 596 1,228 (8 issues need help) 136 Updated Jan 10, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 175 BSD-3-Clause 71 74 26 Updated Jan 10, 2025
  • genetic-prevalence-estimator Public
    broadinstitute/genetic-prevalence-estimator’s past year of commit activity
    Python 1 BSD-3-Clause 0 49 (4 issues need help) 3 Updated Jan 10, 2025
  • str-analysis Public

    Scripts and utilities related to analyzing short tandem repeats (STRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 32 MIT 8 1 0 Updated Jan 10, 2025
  • 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 22 MIT 20 26 4 Updated Jan 10, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 179 AGPL-3.0 89 48 5 Updated Jan 9, 2025
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser’s past year of commit activity
    TypeScript 81 MIT 45 157 (3 issues need help) 18 Updated Jan 9, 2025
  • sam Public

    workbench identity and access management

    broadinstitute/sam’s past year of commit activity
    Scala 42 BSD-3-Clause 12 3 29 Updated Jan 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 Jan 9, 2025
  • mitograph Public
    broadinstitute/mitograph’s past year of commit activity
    Rust 0 0 0 0 Updated Jan 9, 2025
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