Introduction

nf-core/methylseq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

Pipeline Steps

The pipeline allows you to choose between running either Bismark or bwa-meth / MethylDackel. Choose between workflows by using --aligner bismark (default) or --aligner bwameth.

Step	Bismark workflow	bwa-meth workflow
Generate Reference Genome Index (optional)	Bismark	bwa-meth
Raw data QC	FastQC	FastQC
Adapter sequence trimming	Trim Galore!	Trim Galore!
Align Reads	Bismark	bwa-meth
Deduplicate Alignments	Bismark	Picard MarkDuplicates
Extract methylation calls	Bismark	MethylDackel
Sample report	Bismark	-
Summary Report	Bismark	-
Alignment QC	Qualimap	Qualimap
Project Report	MultiQC	MultiQC

Documentation

The nf-core/methylseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation and configuration
2. Running the pipeline
3. Output and how to interpret the results

Credits

These scripts were originally written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden.

• Main author:
  • Phil Ewels (@ewels)
• Contributors:
  • Rickard Hammarén (@Hammarn)
  • Alexander Peltzer (@apeltzer)