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

RNAseq analysis notes from Ming Tang

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

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)

ATLAS - Three commands to start analyzing your metagenome data

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

RNA-seq workflow using STAR and DESeq2

This Snakemake pipeline implements the GATK best-practices workflow

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

The uncompromising Snakemake code formatter

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.

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

MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses

Documentation of the Snakemake-Workflows project

Sequana: a set of Snakemake NGS pipelines

A SingleCell RNASeq pre-processing snakemake workflow

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 - for sampled individuals, and for pool sequencing.

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

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

ATAC-seq snakemake pipeline

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.

Snakemake-based workflow for detecting structural variants in genomic data

🦠🧬🧑‍💻📇 Microbial genomes-to-report pipeline

Monitor computational workflows in real time

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

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.

Configure workflow/pipeline tests using yaml files.