This is the development home of the workflow management system Snakemake. For general information, see

RNAseq analysis notes from Ming Tang

Customizable workflows based on snakemake and python for the analysis of NGS data

ATLAS - Three commands to start analysing your metagenome data

RNA-seq workflow using STAR and DESeq2

A SingleCell RNASeq pre-processing snakemake workflow

This Snakemake pipeline implements the GATK best-practices workflow

A robust, extensible metagenomics pipeline

Sequana: a set of Snakemake NGS pipelines

Documentation of the Snakemake-Workflows project

a snakemake pipeline to process ChIP-seq files from GEO or in-house

🐍 Snakefiles for common RNA-seq data analysis workflows.

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

ATAC-seq snakemake pipeline

The uncompromising Snakemake code formatter

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

A cookiecutter template for Snakemake workflows

Exome/Capture/RNASeq Pipeline Implementation using snakemake

A framework for keeping biomedical text mining result up-to-date

Snakemake-based workflow for detecting structural variants in WGS data

[MIRROR] Emacs support for Snakemake

Snakemake based pipeline for RNA-Seq analysis

reproducible research project template for R using Renv and snakemake with an econ application

A workflow for creating small NGS test data sets, useful for continuous integration.

Snakemake skeleton - Build workflows with Snakemake

Monitor computational workflows in real time

Tutorial with snakemake and Scientific Filesystem