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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 597

  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 993 372

  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 359

Repositories

Showing 10 of 1336 repositories
  • EmmaEmb Public
    broadinstitute/EmmaEmb’s past year of commit activity
    Python 4 MIT 0 0 0 Updated Jan 31, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 61 28 23 16 Updated Jan 31, 2025
  • viral-core Public

    viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux

    broadinstitute/viral-core’s past year of commit activity
    Python 4 1 10 2 Updated Jan 31, 2025
  • viral-baseimage Public

    Broad Viral Genomics base docker image

    broadinstitute/viral-baseimage’s past year of commit activity
    Shell 1 1 1 1 Updated Jan 31, 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 212 MIT 64 7 1 Updated Jan 31, 2025
  • rock-pigean Public

    PIGEAN-related workflows

    broadinstitute/rock-pigean’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Jan 31, 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 Jan 31, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 4 0 1 11 Updated Jan 31, 2025
  • stp_segmentation_wdl Public
    broadinstitute/stp_segmentation_wdl’s past year of commit activity
    WDL 0 0 0 1 Updated Jan 31, 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 9 Updated Jan 31, 2025
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