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
Sample complexity Preseq Preseq
Project Report MultiQC MultiQC


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


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