Untitled ItBISULFITE-SEQ ANALYSIS PIPELINE USING SNAKEMAKE AND BISMARKem

<br>SUMMARY<br>This Snakemake pipeline automates the processing of paired-end bisulfite sequencing datafor methylation analysis in <i>Nasonia vitripennis</i>. It performs adapter trimming, genomepreparation, read alignment (both experimental and lambda controls), methylation extraction,and final CpG merging.<br>CONFIGURATION<br>Sample names must be defined in an external `config.yaml` file:<br>config.yaml:samples: - sample1 - sample2 ...<br>KEY STEPS<br>1. 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 calls<br>RULES OVERVIEW<br>- `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 file<br>REQUIRED MODULES (LOADED IN SHELL COMMANDS)<br>- `py-cutadapt/4.4-jv44fem`- `bowtie2/2.5.1-s4zfmrn`<br>