broadinstitute/long-read-pipelines

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broadinstitute/long-read-pipelines

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Long read production pipelines

Long read pipelines

This repository contains pipelines for processing of long read data from PacBio and/or Oxford Nanopore platforms. The pipelines are written in WDL 1.0 intended for use with Google Cloud Platform via the scientific workflow engine, Cromwell. Processing is designed to be reasonably consistent between both long read platforms, and use platform-specific options or tasks where necessary.

High level workflows can be found in the wdl/ directory.

gatk

Official code repository for GATK versions 4 and up

cromwell

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

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

infercnv

Inferring CNV from Single-Cell RNA-Seq

keras-rcnn

Keras package for region-based convolutional neural networks (RCNNs)

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

pilon

Pilon is an automated genome assembly improvement and variant detection tool

keras-resnet

Keras package for deep residual networks

CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Tangram

Spatial alignment of single cell transcriptomic data.

Jupyter Notebook

ssGSEA2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

warp

WDL Analysis Research Pipelines

viral-ngs

Viral genomics analysis pipelines

seqr

web-based analysis tool for rare disease genomics

gatk-sv

A structural variation pipeline for short-read sequencing

tensorqtl

Ultrafast GPU-enabled QTL mapper

ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

wot

A software package for analyzing snapshots of developmental processes

Jupyter Notebook

ml4h

Jupyter Notebook

depmap_omics

What you need to process the Quarterly DepMap-Omics releases from Terra

xtermcolor

Python library for terminal color support (including 256-color support)

Drop-seq

Java tools for analyzing Drop-seq data

mutect

MuTect -- Accurate and sensitive cancer mutation detection

genomics-in-the-cloud

Source code and related materials for the O'Reilly book

Jupyter Notebook

gnomad_methods

Hail helper functions for the gnomAD project and Translational Genomics Group

pyro-cov

Pyro models of SARS-CoV-2 variants

Jupyter Notebook

catch

A package for designing compact and comprehensive capture probe sets.

gatk-docs

Documentation archive for GATK tools and workflows

oncotator

gnomad-browser

Explore gnomAD datasets on the web

gtex-viz

GTEx Visualizations

single_cell_portal_core

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

PhylogicNDT

docker-terraform

Docker container for running the Terraform application

2020_scWorkshop

Code and data repository for the 2020 physalia course on single cell RNA sequencing.

cromshell

CLI for interacting with Cromwell servers

cellpainting-gallery

Cell Painting Gallery

viral-pipelines

viral-ngs: complete pipelines

gnomad_qc

Jupyter Notebook

single_cell_portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

gistic2

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2

sam

workbench identity and access management

dsde-deep-learning

DSDE Deep Learning Club

gamgee

A C++14 library for NGS data formats

wdl-ide

Rich IDE support for Workflow Description Language

gtex-v8

Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper

Jupyter Notebook

pyqtl

Collection of analysis tools for quantitative trait loci

SignatureAnalyzer-GPU

GPU implementation of ARD NMF

poasta

Fast and exact gap-affine partial order alignment

Celligner_ms

Code related to the Celligner manuscript

cell-health

Predicting Cell Health with Morphological Profiles

PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead

StrainGE

strain-level analysis tools

firecloud-orchestration

gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons

python-cert_manager

Python interface to the Sectigo Certificate Manager REST API

str-analysis

Scripts and utilities related to analyzing short tandem repeats (STRs).

adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.

2019_scWorkshop

Repo for Physalia course Analysis of Single Cell RNA-Seq data

chronos

Modeling of time series data for CRISPR KO experiments

fiss

FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine

pyfrost

Python bindings for Bifrost with a NetworkX compatible API

single_cell_analysis

Documents used for workshops on single cell analysis

deepometry

Image classification for imaging flow cytometry.

lincs-cell-painting

Processed Cell Painting Data for the LINCS Drug Repurposing Project

Jupyter Notebook

rawls

Rawls service for DSDE

delphy

Fast, scalable, accurate and accessible Bayesian phylogenetics

firepony

Efficient base quality score recalibrator for NGS data

protigy

Proteomics Toolset for Integrative Data Analysis

GATK-for-Microbes

seqr-loading-pipelines

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

BipolarCell2016

cromwell-tools

A collection of Python clients and accessory scripts for interacting with the Cromwell

covid19-testing

COVID-19 Diagnostic Processing Dashboard

single_cell_classification

Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles

VariantBam

Filtering and profiling of next-generational sequencing data using region-specific rules

longbow

Annotation and segmentation of MAS-seq data

gtex-single-nucleus-reference

Code repository for the snRNA-seq cross-tissue atlas project

Jupyter Notebook

flipbook

A tool that lets you quickly flip through images in a local directory and record notes or answer questions about each one.

AwesomeGenomics

Cancer Data Science's go to place for excellent genomics tools and packages

firecloud-ui

FireCloud user interface for web browsers.

BARD

BioAssay Research Database

wdltool

vim-wdl

Vim syntax highlighting for WDL

SpliceAI-lookup

Website for checking SpliceAI and Pangolin scores:

palantir-workflows

Utility workflows for the DSP hydro.gen team (formerly palantir)

epi-SHARE-seq-pipeline

Epigenomics Program pipeline to analyze SHARE-seq data.

wordpress-crowd-plugin

Crowd Authentication Plugin for Wordpress

mix_seq_ms

Code associated with MIX-seq manuscript

imaging-platform-pipelines

Cell Painting and other pipelines from the Imaging Platform

wdl-runner

Easily run WDL workflows on GCP

widdler

A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.

cms

Composite of Multiple Signals: tests for selection in meiotically recombinant populations

regional_missense_constraint

Code to calculate regional missense constraint

scRNA-Seq

scalable_analytics

Public collaboration of Scalable Single Cell Analytics

ml4ht_data_source

Multimodal data loader compatible with pytorch and tensorflow

gene-hints

Discoverability for gene search 🧬 🔍