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

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))

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

RNA-seq workflow using STAR and DESeq2

This Snakemake pipeline implements the GATK best-practices workflow

💎 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

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.

Documentation of the Snakemake-Workflows project

The uncompromising Snakemake code formatter

A SingleCell RNASeq pre-processing snakemake workflow

Sequana: a set of Snakemake NGS pipelines

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

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

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

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

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.