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katwre / makeWGBSnake

Snakemake pipeline for WGBS analysis (private repository)

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This is a private repository that contains a pipeline for WGBS data analysis.

What does it do

  • Raw data QC using FastQC
  • Adapter sequence trimming using Trim Galore!
  • It can subset reads using bbmap (optional)
  • Generate Reference Genome Index (optional)
  • Align Reads using either bismark, bwa-meth or bsmap
  • Merge lanes
  • Deduplicate Alignments using Picard MarkDuplicate
  • Extract methylation calls using either methylKit or methyldacker (CpG, CHH and/or CHG contexts)
  • filter methylation calles and unite common CpGs over all samples using methylKit
  • Create BigWig files
  • Segmentation of methylation signal using methylKit

Example visualisation of the DAG of jobs

Example dag for a pipeline that uses bwa-meth+methyldacker: DAG

About

Snakemake pipeline for WGBS analysis (private repository)

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