SeqPipe (snakemake edition)

A sequencing pipeline based on Snakemake.

Installation

Install Snakemake in order to run the pipeline:

$ pip install snakemake

Furthermore, the following software is used:

• gzip
• FastQC
• BWA
• samtools
• cutadapt
• python 3.6
  • pysam
  • matplotlib
  • matplotlib_venn

Usage

Set up config.yaml to your liking and execute the pipeline as follows:

$ snakemake -p

Create an overview of the pipeline:

$ snakemake --dag | dot -Tpng > overview.png

An exemplary pipeline DAG for aligning reads of the samples A and B to the references test and test2 can be seen below.

Notes

Paired-end reads handling

This pipeline supports mapping single-end as well as paired-end reads. It is assumed that paired-end reads are denoted using R{1,2} (e.g. foo_R1.fastq.gz and foo_R2.fastq.gz). The corresponding results can then be found under the R1 sample.