bio-workflows-methylation-pipeline

Or fastp with conservative settings

fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz
-o trimmed/sample_R1.fq.gz -O trimmed/sample_R2.fq.gz
--detect_adapter_for_pe
--qualified_quality_phred 20
--length_required 35
--html qc/sample_fastp.html

## Prepare genome (once)

bismark_genome_preparation --bowtie2 genome/

## Align

bismark --genome genome/ \
    -1 trimmed/sample_R1_val_1.fq.gz \
    -2 trimmed/sample_R2_val_2.fq.gz \
    -o aligned/ \
    --parallel 4 \
    --temp_dir tmp/