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fastp

Ultra-fast all-in-one FASTQ preprocessor for quality control

brewmacoslinux

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About

Ultra-fast all-in-one FASTQ preprocessor

Commands

fastp

Examples

Basic quality control on paired-end FASTQ files$ fastp -i read1.fastq -I read2.fastq -o out1.fastq -O out2.fastq

Trim adapters and low-quality bases with HTML report$ fastp -i input.fastq -o output.fastq --adapter_sequence AGATCGGAAGAGC -h report.html

Filter reads by length and quality, generate JSON statistics$ fastp -i input.fastq -o output.fastq --length_required 50 --qualified_quality_phred 20 -j stats.json