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

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

💎 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 SingleCell RNASeq pre-processing snakemake workflow

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.

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

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

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