maxplanck-ie/snakepipes

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

Tools to process and analyze deep sequencing data.

A workflow language for data-driven computational pipelines

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

RNA-seq workflow using STAR and DESeq2

Tools for working with genomic and high throughput sequencing data.

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Tools (written in C using htslib) for manipulating next-generation sequencing data