Broad Institute

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1.3k repositories

cromwell
Public
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
docker application cloud bioinformatics scala executor hpc containers wdl ga4gh
Scala
•
BSD 3-Clause "New" or "Revised" License
•359•1k•744•48•Updated Feb 11, 2025Feb 11, 2025
long-read-pipelines
Public
Long read production pipelines
pipelines wdl variant-calling de-novo-assembly long-reads
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•24•143•95•27•Updated Feb 11, 2025Feb 11, 2025
firecloud-orchestration
Public
Scala
•
BSD 3-Clause "New" or "Revised" License
•4•31•0•4•Updated Feb 11, 2025Feb 11, 2025
datarepo-helm
Public
A helm repo for Broad Data Science Platforms helm charts
Mustache
•1•5•0•3•Updated Feb 11, 2025Feb 11, 2025
cds-daintree
Public
Python
•0•0•0•1•Updated Feb 11, 2025Feb 11, 2025
juniper
Public
Java
•
BSD 3-Clause "New" or "Revised" License
•5•9•0•16•Updated Feb 11, 2025Feb 11, 2025
gatk
Public
Official code repository for GATK versions 4 and up
science bioinformatics genomics genome ngs sequencing dna spark gatk
Java
•
Other
•596•1.8k•1.2k•137•Updated Feb 11, 2025Feb 11, 2025
BEClust3D
Public
Jupyter Notebook
•
Other
•0•0•0•8•Updated Feb 11, 2025Feb 11, 2025
2024-09-27-python-intro-lesson
Public
Based on https://github.com/librarycarpentry/lc-python-intro/
HTML
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Other
•1•0•0•1•Updated Feb 11, 2025Feb 11, 2025
2024-09-20-unix-shell-lesson
Public
Based on https://github.com/datacarpentry/shell-genomics/
R
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Other
•0•0•0•0•Updated Feb 11, 2025Feb 11, 2025
rawls
Public
Rawls service for DSDE
Scala
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BSD 3-Clause "New" or "Revised" License
•4•26•0•12•Updated Feb 11, 2025Feb 11, 2025
carmen-analysis
Public
Python
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MIT License
•0•4•0•0•Updated Feb 10, 2025Feb 10, 2025
puppet-sentinelone_agent
Public
Puppet module to manage the SentinelOne agent
Ruby
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BSD 3-Clause "New" or "Revised" License
•2•1•1•1•Updated Feb 10, 2025Feb 10, 2025
SpliceAI-lookup
Public
Website for checking SpliceAI and Pangolin scores:
pangolin spliceai
HTML
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MIT License
•7•20•3•0•Updated Feb 10, 2025Feb 10, 2025
exome-results-browsers
Public
Results browsers for case-control studies of psychiatric diseases done at the Broad Institute
JavaScript
•
BSD 3-Clause "New" or "Revised" License
•4•11•7•3•Updated Feb 10, 2025Feb 10, 2025
depmap-portal
Public
Code for the DepMap portal at depmap.org
Python
•
BSD 2-Clause "Simplified" License
•1•7•0•9•Updated Feb 10, 2025Feb 10, 2025
seqr-loading-pipelines
Public
hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
Python
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MIT License
•20•23•24•6•Updated Feb 10, 2025Feb 10, 2025
dig-dug-portal
Public
Vue
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BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Feb 10, 2025Feb 10, 2025
backstage
Public
Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
TypeScript
•0•2•4•5•Updated Feb 10, 2025Feb 10, 2025
gnomad_methods
Public
Hail helper functions for the gnomAD project and Translational Genomics Group
genomics genomes exomes hail
Python
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MIT License
•29•92•8•7•Updated Feb 10, 2025Feb 10, 2025
sam
Public
workbench identity and access management
Scala
•
BSD 3-Clause "New" or "Revised" License
•12•42•3•30•Updated Feb 10, 2025Feb 10, 2025
workbench-libs
Public
Workbench utility libraries
Scala
•
Other
•4•9•0•2•Updated Feb 10, 2025Feb 10, 2025
gnomad-browser
Public
Explore gnomAD datasets on the web
javascript genomics gnomad
TypeScript
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MIT License
•45•81•162•14•Updated Feb 10, 2025Feb 10, 2025
warp
Public
WDL Analysis Research Pipelines
WDL
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BSD 3-Clause "New" or "Revised" License
•100•208•7•17•Updated Feb 10, 2025Feb 10, 2025
celldega
Public
Spatial omics analysis and visualization library
Jupyter Notebook
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Other
•0•4•1•12•Updated Feb 10, 2025Feb 10, 2025
gatk-sv
Public
A structural variation pipeline for short-read sequencing
bioinformatics genomics structural-variation structural-variants
Python
•
BSD 3-Clause "New" or "Revised" License
•72•178•74•21•Updated Feb 10, 2025Feb 10, 2025
ops-terra-utils
Public
Python
•0•4•0•4•Updated Feb 10, 2025Feb 10, 2025
shared-workflows
Public
GitHub Action workflows that can be shared by multiple repositories
BSD 3-Clause "New" or "Revised" License
•1•0•3•0•Updated Feb 10, 2025Feb 10, 2025
glama
Public
Genomic long-read analysis modules and applications
Rust
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•2•Updated Feb 10, 2025Feb 10, 2025
jump-profiling-recipe
Public
Workflow for processing cpg0016-jump profiles
Python
•
BSD 3-Clause "New" or "Revised" License
•7•2•8•2•Updated Feb 10, 2025Feb 10, 2025