RESEARCH USE
Where fastp fits
fastp can provide a combined preprocessing step before short-read alignment or quantification. It summarizes read quality, trims adapters or low-quality bases, applies configurable filters, handles paired reads, and writes HTML and JSON reports. Retain the original FASTQ files, full command, version, and reports, and compare read counts and quality distributions before and after processing.
Research tasks
- Inspect and preprocess single-end or paired-end FASTQ data
- Trim adapters, low-quality bases, and specified sequences
- Generate archivable quality-control reports
What to evaluate before use
- The project positions fastp primarily for short reads such as Illumina and MGI data; evaluate fastplong or another dedicated workflow for long reads.
- Default filters and automatic adapter detection are not suitable for every library. Trimming changes the observations, so retain the raw files and document all settings.
Verification note
This entry summarizes the tool's role without assessing scientific accuracy or endorsing its outputs. Features and terms can change; consult the official source before adopting it for consequential work.
FASTQ preprocessingshort-read sequencing
Last verified: 2026-09-07
Source: official documentation ↗