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.

StepBismark workflowbwa-meth workflow
Generate Reference Genome Index (optional)Bismarkbwa-meth
Raw data QCFastQCFastQC
Adapter sequence trimmingTrim Galore!Trim Galore!
Align ReadsBismarkbwa-meth
Deduplicate AlignmentsBismarkPicard MarkDuplicates
Extract methylation callsBismarkMethylDackel
Sample reportBismark-
Summary ReportBismark-
Alignment QCQualimapQualimap
Sample complexityPreseqPreseq
Project ReportMultiQCMultiQC


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.