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 analyzing your metagenome data

RNA-seq workflow using STAR and DESeq2

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

This Snakemake pipeline implements the GATK best-practices workflow

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

A robust, extensible metagenomics pipeline

Documentation of the Snakemake-Workflows project

A SingleCell RNASeq pre-processing snakemake workflow

Automated and customizable 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.

Sequana: a set of Snakemake NGS pipelines

The uncompromising Snakemake code formatter

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

A simple Snakemake profile for Slurm without --cluster-config

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

🐍 Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.