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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 604

  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 373

  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 361

Repositories

Showing 10 of 1374 repositories
  • 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 1 0 0 Updated Apr 15, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 16 Updated Apr 15, 2025
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 69 BSD-3-Clause 27 6 11 Updated Apr 15, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,791 604 1,243 (8 issues need help) 139 Updated Apr 15, 2025
  • 2024-09-27-python-intro-lesson Public

    Based on https://github.com/librarycarpentry/lc-python-intro/

    broadinstitute/2024-09-27-python-intro-lesson’s past year of commit activity
    HTML 0 1 0 2 Updated Apr 15, 2025
  • 2024-09-20-unix-shell-lesson Public

    Based on https://github.com/datacarpentry/shell-genomics/

    broadinstitute/2024-09-20-unix-shell-lesson’s past year of commit activity
    R 0 0 0 1 Updated Apr 15, 2025
  • puppet-sentinelone_agent Public

    Puppet module to manage the SentinelOne agent

    broadinstitute/puppet-sentinelone_agent’s past year of commit activity
    Ruby 2 BSD-3-Clause 3 1 2 Updated Apr 14, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 14 Updated Apr 14, 2025
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 0 2 Updated Apr 14, 2025
  • 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 6 MIT 0 1 1 Updated Apr 14, 2025
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