Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
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Build Status Nextflow Gitter

install with bioconda Docker Container available Singularity Container available


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.

Choice of workflows

There are two separate workflows contained in this repository - one using Bismark and one using bwa-meth / MethylDackel. The Bismark pipeline is being actively developed and maintained, the bwa-meth workflow is not (currently). The Nextflow manifest specifies the Bismark pipeline as the default workflow, so the bwa-meth script will be ignored unless explicitly run.


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.

Participating Institutes

nf-core/methylseq is used by a number of core sequencing and bioinformatics facilities. Some of these are listed below. If you use this pipeline too, please let us know in an issue and we will add you to the list.

SciLifeLab National Genomics Infrastructure (NGI), Sweden
Quantitative Biology Center (QBiC), Germany