snakemake

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

This Snakemake pipeline implements the GATK best-practices workflow

PyPSA-Eur: An Open Optimisation Model of the European Transmission System

A robust, extensible metagenomics pipeline

Documentation of the Snakemake-Workflows project

A SingleCell RNASeq pre-processing snakemake workflow

Sequana: a set of Snakemake NGS pipelines

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.

The uncompromising Snakemake code formatter

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

💎 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 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.

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.

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