DNA Methylation Sequence Alignment with Bismark

Overview

This skill performs bisulfite-aware sequence alignment for DNA methylation sequencing using Bismark only. It is designed for autonomous execution from FASTQ input through aligned BAM generation and basic QC, while preventing unsafe assumptions about genome build, library layout, or assay design.

Main steps include:

• Refer to the Inputs & Outputs section and create the output architecture in Step 0.
• Always ask the user for the reference genome directory to use for Bismark. Never infer genome build from filenames alone.
• Always ask the user whether the assay is WGBS, RRBS, or another bisulfite-based methylation assay if that affects trimming or downstream interpretation and is not already known.
• Detect whether input data are paired-end or single-end.
• Group FASTQ files into samples using naming conventions.
• Validate that the Bismark genome folder has been prepared.
• Run Bismark alignment.
• Sort and index BAM output with samtools.
• Generate basic alignment QC reports and write a parameter log file for every sample.
• Keep the workflow alignment-focused; methylation extraction belongs in a downstream skill.