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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 603

  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 1365 repositories
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 7 BSD-2-Clause 1 0 9 Updated Apr 5, 2025
  • starrynight Public

    Library and tools to process optical pooled screening datasets

    broadinstitute/starrynight’s past year of commit activity
    Python 2 BSD-3-Clause 0 27 2 Updated Apr 5, 2025
  • hidive Public
    broadinstitute/hidive’s past year of commit activity
    Rust 0 BSD-3-Clause 0 5 1 Updated Apr 4, 2025
  • ABC-Enhancer-Gene-Prediction Public

    Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

    broadinstitute/ABC-Enhancer-Gene-Prediction’s past year of commit activity
    Python 218 MIT 67 5 0 Updated Apr 4, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 185 AGPL-3.0 90 53 3 Updated Apr 4, 2025
  • jati Public

    DSL support library for Rust

    broadinstitute/jati’s past year of commit activity
    Rust 1 BSD-3-Clause 0 0 0 Updated Apr 4, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 1 Updated Apr 4, 2025
  • cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,011 BSD-3-Clause 361 745 48 Updated Apr 4, 2025
  • EmmaEmb Public
    broadinstitute/EmmaEmb’s past year of commit activity
    Python 11 MIT 0 0 0 Updated Apr 4, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 186 BSD-3-Clause 75 80 21 Updated Apr 4, 2025
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