Repositories list

• str-analysis

  Public
  Scripts and utilities for analyzing tandem repeats (TRs).

  Python

  •

  MIT License

  •11•42•0•0•Updated Mar 5, 2026Mar 5, 2026

• TRExplorer

  Public
  An online portal for exploring tandem repeats (TRs) genome-wide.

  HTML

  •

  MIT License

  •0•1•5•0•Updated Mar 5, 2026Mar 5, 2026

• dsp-appsec-infrastructure-apps

  Public
  This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

  securityapplication-securityappsec+ 10

  securityapplication-securityappsecsecurity-scannersecure-developmentsecurity-automationsecurity-toolsdevsecopssecurity-scanappsecurity+ 3

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•7•0•11•Updated Mar 5, 2026Mar 5, 2026

• permutect

  Public
  Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

  Python

  •

  Apache License 2.0

  •2•10•10•11•Updated Mar 5, 2026Mar 5, 2026

• genohype

  Public
  Rust

  •0•0•0•5•Updated Mar 5, 2026Mar 5, 2026

• hail-rust-decoder

  Public
  Rust

  •0•1•0•5•Updated Mar 5, 2026Mar 5, 2026

• all-by-all-aou-browser

  Public
  TypeScript

  •0•0•0•4•Updated Mar 5, 2026Mar 5, 2026

• viral-pipelines

  Public
  viral-ngs: complete pipelines

  WDL

  •

  Other

  •30•73•21•20•Updated Mar 5, 2026Mar 5, 2026

• liverkp-assets

  Public
  Share assets for the Liver KP

  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

• trexplorer-catalog

  Public

  broadinstitute/trexplorer-catalog’s past year of commit activity
  Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]

  Python

  •

  MIT License

  •1•17•1•0•Updated Mar 5, 2026Mar 5, 2026

• depmap-portal

  Public
  Code for the DepMap portal at depmap.org

  TypeScript

  •

  BSD 2-Clause "Simplified" License

  •1•8•1•10•Updated Mar 4, 2026Mar 4, 2026

• qprimer_designer

  Public
  Design tool for highly performant qPCR diagnostics.

  Python

  •

  MIT License

  •1•4•1•0•Updated Mar 4, 2026Mar 4, 2026

• workflow-dispatch

  Public
  A GitHub Action for triggering workflows, using the `workflow_dispatch` event

  JavaScript

  •

  MIT License

  •139•0•0•1•Updated Mar 4, 2026Mar 4, 2026

• Drop-seq

  Public
  Java tools for analyzing Drop-seq data

  Jupyter Notebook

  •

  MIT License

  •35•133•11•0•Updated Mar 4, 2026Mar 4, 2026

• dig-dug-portal

  Public
  Vue

  •

  BSD 3-Clause "New" or "Revised" License

  •2•2•0•0•Updated Mar 4, 2026Mar 4, 2026

• seqr

  Public
  web-based analysis tool for rare disease genomics

  Python

  •

  GNU Affero General Public License v3.0

  •93•201•45•15•Updated Mar 4, 2026Mar 4, 2026

• gnomad-browser

  Public
  Explore gnomAD datasets on the web

  javascriptgenomicsgnomad

  javascriptgenomicsgnomad

  TypeScript

  •

  MIT License

  •49•86•165•16•Updated Mar 4, 2026Mar 4, 2026

• seqr-helm

  Public
  Helm charts for the seqr project

  Go Template

  •

  BSD 3-Clause "New" or "Revised" License

  •5•3•5•2•Updated Mar 4, 2026Mar 4, 2026

• bican-mccarroll-manuscript1

  Public
  Scripts used to process data for the first McCarroll lab BICAN manuscript

  R

  •

  MIT License

  •0•0•0•2•Updated Mar 4, 2026Mar 4, 2026

• warp

  Public
  Warp Analysis Research Pipelines

  WDL

  •

  BSD 3-Clause "New" or "Revised" License

  •112•225•7•10•Updated Mar 4, 2026Mar 4, 2026

• viral-ngs

  Public
  viral-ngs: command line tools and wrappers for processing raw viral genomic data

  pythondockerbioinformatics+ 12

  pythondockerbioinformaticsgenomicsgenomengsvariant-callingbamgenome-sequencingillumina+ 5

  Python

  •

  MIT License

  •67•194•2•0•Updated Mar 4, 2026Mar 4, 2026

• gatk

  Public
  Official code repository for GATK versions 4 and up

  sciencebioinformaticsspark+ 6

  sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk

  Java

  •

  Other

  •624•1.9k•1.3k•149•Updated Mar 4, 2026Mar 4, 2026

• seqr-loading-pipelines

  Public
  hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

  Python

  •

  MIT License

  •23•23•20•4•Updated Mar 4, 2026Mar 4, 2026

• dig-aggregator-methods

  Public
  Monorepo of methods implemented for the Aggregator

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•1•0•9•Updated Mar 4, 2026Mar 4, 2026

• cromwell

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

  dockerapplicationworkflow+ 10

  dockerapplicationworkflowcloudbioinformaticsscalaexecutorhpccontainerswdl+ 3

  Scala

  •

  BSD 3-Clause "New" or "Revised" License

  •378•1.1k•759•50•Updated Mar 4, 2026Mar 4, 2026

• juniper

  Public
  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •5•9•0•21•Updated Mar 4, 2026Mar 4, 2026

• delphy

  Public
  Fast, scalable, accurate and accessible Bayesian phylogenetics

  C++

  •

  MIT License

  •4•42•0•0•Updated Mar 4, 2026Mar 4, 2026

• bcftools-patched

  Public
  WDL workflows for patched bcftools with GCS resilience fixes

  WDL

  •0•1•0•0•Updated Mar 4, 2026Mar 4, 2026

• gnomad_qc

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •29•69•5•16•Updated Mar 4, 2026Mar 4, 2026

• single_cell_portal_core

  Public
  Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

  rna-seq-analysissingle-cell-genomicshuman-cell-atlas

  rna-seq-analysissingle-cell-genomicshuman-cell-atlas

  Ruby

  •

  BSD 3-Clause "New" or "Revised" License

  •27•70•0•2•Updated Mar 4, 2026Mar 4, 2026