Bismark Alignment

Prepare Genome Index

# One-time genome preparation (creates bisulfite-converted index)
bismark_genome_preparation --bowtie2 /path/to/genome_folder/

# Genome folder should contain FASTA files (e.g., hg38.fa, chr1.fa, etc.)
# Creates Bisulfite_Genome/ subdirectory with CT and GA converted indices

Basic Single-End Alignment

bismark --genome /path/to/genome_folder/ reads.fastq.gz -o output_dir/

Paired-End Alignment