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    1.3k repositories

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •594•1.7k•1.2k•137•Updated Nov 24, 2024Nov 24, 2024

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•7•Updated Nov 24, 2024Nov 24, 2024

    • stp_segmentation_wdl

      Public
      WDL
      •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•31•5•Updated Nov 23, 2024Nov 23, 2024

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •96•202•7•13•Updated Nov 23, 2024Nov 23, 2024

    • heimdall

      Public
      Shell
      •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • juniper0

      Public
      Preliminary Version of JUNIPER: Large-Scale Outbreak Reconstruction
      R
      •
      MIT License
      •0•2•0•0•Updated Nov 23, 2024Nov 23, 2024

    • molecular-data-provider

      Public
      Molecular Data Provider
      Python
      •
      MIT License
      •8•11•3•5•Updated Nov 22, 2024Nov 22, 2024

    • lembic

      Public
      Distilling some data for CFDE
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationcloudbioinformaticsscalaexecutorhpccontainerswdlga4gh
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •361•999•744•48•Updated Nov 22, 2024Nov 22, 2024

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•176•53•4•Updated Nov 22, 2024Nov 22, 2024

    • thurloe

      Public
      A simple service to store arbitrary key/value pairs
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•4•Updated Nov 22, 2024Nov 22, 2024

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•13•Updated Nov 22, 2024Nov 22, 2024

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •24•142•95•26•Updated Nov 22, 2024Nov 22, 2024

    • ops-terra-utils

      Public
      Python
      •0•3•0•2•Updated Nov 22, 2024Nov 22, 2024

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•7•Updated Nov 22, 2024Nov 22, 2024

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•9•Updated Nov 22, 2024Nov 22, 2024

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•9•1•10•Updated Nov 22, 2024Nov 22, 2024

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •27•62•23•17•Updated Nov 22, 2024Nov 22, 2024

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Nov 22, 2024Nov 22, 2024

    • delphy

      Public
      Fast, scalable, accurate and accessible Bayesian phylogenetics
      C++
      •
      Other
      •3•27•0•0•Updated Nov 22, 2024Nov 22, 2024

    • cromwell-develop

      Public
      Repository for Broad specific cromwell **configs**. For the cromwell software, see https://github.com/broadinstitute/cromwell
      Shell
      •0•1•0•0•Updated Nov 22, 2024Nov 22, 2024

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •8•19•4•4•Updated Nov 22, 2024Nov 22, 2024

    • dsp-reusable-workflows

      Public
      publicly available reusable workflows
      Python
      •0•0•0•4•Updated Nov 22, 2024Nov 22, 2024

    • 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
      •
      MIT License
      •368•984•200•18•Updated Nov 22, 2024Nov 22, 2024

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•1•Updated Nov 22, 2024Nov 22, 2024

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•28•Updated Nov 22, 2024Nov 22, 2024

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •44•80•160•13•Updated Nov 22, 2024Nov 22, 2024

    • gnomad-blog

      Public
      Blog for the gnomAD project
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•7•2•Updated Nov 22, 2024Nov 22, 2024

    • ist_benchmarking

      Public
      Jupyter Notebook
      •0•0•0•1•Updated Nov 22, 2024Nov 22, 2024