OpenGene/fastp

Health v2 · maintenance only

Adoption not part of the score

2435 stars · 389 forks observed · 2026-10-07

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

fastp is an ultra-fast all-in-one FASTQ preprocessing and quality control tool written in C++. It handles adapter trimming, quality filtering, read splitting/merging, UMI processing, and QC reporting for short-read sequencing data.

Use cases

• trim adapters from Illumina FASTQ reads
• quality control and filtering of NGS sequencing data
• preprocess FASTQ files before alignment
• remove low-quality reads and polyG tails
• split and merge paired-end FASTQ files
• extract UMIs from sequencing reads
• generate QC reports for FASTQ data

When to choose

• you need fast, single-tool FASTQ preprocessing for short reads
• you want combined trimming, filtering, and QC reporting in one step
• you work with Illumina or MGI sequencing data
• you need batch processing of many FASTQ files

When to avoid

• you are processing long reads from Nanopore or PacBio (use fastplong instead)
• you need highly specialized trimming algorithms not covered by fastp
• you require a GUI-only workflow

Facets

cli-tool · maturity stable

cli developer-tools bioinformatics windows cli cross-platform fastq quality-control adapter-trimming ngs sequencing illumina umi bioinformatics data-engineering command-line linux macos

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markdown · JSON · MCP: product_card(name="OpenGene/fastp")