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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 1.8k 602

  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 372

  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 1354 repositories
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 145 BSD-3-Clause 25 95 (2 issues need help) 26 Updated Mar 23, 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 25 2 Updated Mar 23, 2025
  • xipher Public

    Tools for calling X-inactivation in scRNA-seq data

    broadinstitute/xipher’s past year of commit activity
    R 0 MIT 0 0 0 Updated Mar 23, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 Updated Mar 22, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,783 602 1,239 (8 issues need help) 131 Updated Mar 22, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 10 Updated Mar 22, 2025
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    broadinstitute/dig-aggregator-methods’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 7 Updated Mar 22, 2025
  • pbs-analysis Public

    Scripts for analyzing ChIP-seq and related datatypes with binning and PBS

    broadinstitute/pbs-analysis’s past year of commit activity
    R 1 1 1 1 Updated Mar 22, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 185 AGPL-3.0 89 48 4 Updated Mar 22, 2025
  • 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 7 Updated Mar 22, 2025
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