snakemake

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

RNAseq analysis notes from Ming Tang

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

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

💎 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

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

The uncompromising Snakemake code formatter

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

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

A SingleCell RNASeq pre-processing snakemake workflow

Sequana: a set of Snakemake NGS pipelines

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.