pipeline-wgbslisted

# ENCODE WGBS Pipeline: FASTQ to Methylation Calls ## When to Use - User wants to run a WGBS/bisulfite sequencing pipeline from FASTQ to methylation calls - User asks about "WGBS pipeline", "bisulfite sequencing", "methylation calling", "Bismark", or "bedMethyl" - User needs to process whole-genome bisulfite sequencing data following ENCODE standards - Example queries: "process my WGBS FASTQs", "call methylation levels from bisulfite-seq", "run Bismark on my WGBS data" Execute the ENCODE DNA methylation pipeline for Whole Genome Bisulfite Sequencing data, producing per-CpG methylation levels in bedMethyl format. ## Pipeline Overview ``` FASTQ -> Trim adapters -> Bismark align -> Deduplicate -> MethylDackel extract -> bedMethyl | | | | | | QC Trim Galore Bismark/bwa-meth Picard Per-CpG calls Final output ``` ### ENCODE Repository - **GitHub**: `ENCODE-DCC/dna-me-pipeline` - **Container**: `encodedcc/dna-me-pipeline` - **WDL**: Available for Cromwell execution - **This skill**: Nextflow DSL2 reimplementation for portability ## Core Tools and Versions | Tool | Version | Purpose | Citation | |------|---------|---------|----------| | Trim Galore | 0.6.10 | Adapter + quality trimming (bisulfite-aware) | Krueger (Babraham) | | Bismark | 0.24.2 | Bisulfite-aware alignment + methylation | Krueger & Andrews 2011 | | bwa-meth | 0.2.7 | Alternative bisulfite aligner (faster) | Ped