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