Execute whole genome methylation sequencing pipelines
pipeline-wgbsskillsetup L4★35
ammawla/encode-toolkit ↗What it does
Call DNA methylation levels from bisulfite-seq data
Best for
Generating publication-ready methylation maps from whole-genome bisulfite sequencing following ENCODE methylation standards.
Inputs
- · Paired-end FASTQ files
- · Bismark-indexed reference genome
Outputs
- · bedMethyl files (per-CpG methylation)
- · Conversion rate QC
- · Coverage statistics
Requires
- · Trim Galore
- · Bismark
- · MethylDackel
- · Picard
- · samtools
Preconditions
- · Nextflow DSL2
- · WGBS strandedness (dUTP standard)
- · Lambda/pUC19 spike-in for QC
Failure modes
- · Bisulfite conversion rate <95%
- · Low CpG coverage (<5x)
- · High duplication rate (>50%)
Trust signals
- · ENCODE DNA methylation standards
- · Bisulfite-aware trimming
- · Conversion rate QC