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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 1.7k 594

  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 984 369

  3. cromwell cromwell Public

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

    Scala 999 360

Repositories

Showing 10 of 1322 repositories
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 2 Updated Nov 28, 2024
  • 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 30 (1 issue needs help) 1 Updated Nov 28, 2024
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 8 BSD-3-Clause 5 0 7 Updated Nov 28, 2024
  • 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 8 Updated Nov 27, 2024
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 123 23 30 (1 issue needs help) 20 Updated Nov 27, 2024
  • lembic Public

    Distilling some data for CFDE

    broadinstitute/lembic’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Nov 27, 2024
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 177 AGPL-3.0 89 47 3 Updated Nov 27, 2024
  • poasta Public

    Fast and exact gap-affine partial order alignment

    broadinstitute/poasta’s past year of commit activity
    Rust 40 BSD-3-Clause 2 7 2 Updated Nov 27, 2024
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 172 BSD-3-Clause 70 73 22 Updated Nov 27, 2024
  • DBP_Doe Public

    files that will be used to train the 3D Unet on CHTC

    broadinstitute/DBP_Doe’s past year of commit activity
    Python 0 0 0 0 Updated Nov 27, 2024
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