BISULFITE-SEQ ANALYSIS PIPELINE USING SNAKEMAKE AND BISMARK

SUMMARYThis Snakemake pipeline automates the processing of paired-end bisulfite sequencing datafor methylation analysis in Nasonia vitripennis. It performs adapter trimming, genomepreparation, read alignment (both experimental and lambda controls), methylation extraction,and final CpG merging.CONFIGURATIONSample names must be defined in an external `config.yaml` file:config.yaml:samples: - sample1 - sample2 ...KEY STEPS1. Trimming: Adapter trimming and quality filtering using `cutadapt`2. Genome Preparation: Bismark-compatible indexing of both experimental and lambda genomes3. Alignment: Paired-end alignment using `bismark` with Bowtie24. Methylation Extraction: Extract methylation calls from BAM files5. CpG Merging: Collapse strand-specific CpG methylation into unified callsRULES OVERVIEW- `all`: Defines final output files to build for all samples- `trimming`: Trims adapters from raw fastq files- `genome_prep`: Prepares the experimental genome for Bismark- `lambda_genome_prep`: Prepares the lambda genome for control alignment- `alignment`: Aligns reads to the experimental genome- `lambda_alignment`: Aligns reads to the lambda genome (conversion rate check)- `meth_extraction`: Extracts methylation data from aligned BAM- `merge_cpgs`: Merges complementary CpG calls into a single output fileREQUIRED MODULES (LOADED IN SHELL COMMANDS)- `py-cutadapt/4.4-jv44fem`- `bowtie2/2.5.1-s4zfmrn`