fastp — Fast FASTQ Quality Control and Adapter Trimming

Overview

fastp performs adapter trimming, quality filtering, and QC reporting for Illumina FASTQ files in a single multi-threaded pass. It automatically detects adapter sequences from paired-end read overlaps — eliminating the need to specify adapters manually. fastp corrects mismatches in paired-end overlap regions, filters reads by quality score and length, removes polyX tails (polyA for RNA-seq), and generates interactive HTML and machine-readable JSON QC reports. Being 3–10× faster than Trim Galore and Trimmomatic while providing comparable or better results, fastp has become the standard preprocessing step before alignment in WGS, RNA-seq, and ChIP-seq pipelines.

When to Use

• Trimming Illumina adapters and low-quality bases before alignment in any NGS pipeline (RNA-seq, WGS, WES, ChIP-seq, ATAC-seq)
• Generating per-sample QC reports (HTML + JSON) as the first step of a pipeline, before MultiQC aggregation
• Processing paired-end reads where adapter auto-detection from overlap is preferred over manual adapter specification
• Removing polyA tails from RNA-seq reads from 3′ end-enriched protocols (Smart-seq, QuantSeq)
• Splitting a FASTQ file by UMI or by index for demultiplexing workflows
• Use Trim Galore as an alternative when TrimGalore's detailed per-base quality report from FastQC is required alongside trimming
• Use Trimmomatic as an alternative for fine-grained control of sliding-window trimming steps

Prerequisites