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An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

Bioconductor version: Release (3.19)

Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.

Author: Wei Wang [aut] , Ji-Dung Luo [ctb] , Thomas Carroll [cre, aut]

Maintainer: Thomas Carroll <tc.infomatics at>

Citation (from within R, enter citation("Rfastp")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Rfastp HTML R Script
Reference Manual PDF


biocViews Preprocessing, QualityControl, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3 + file LICENSE
Imports Rcpp, rjson, ggplot2, reshape2
System Requirements GNU make
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Suggests BiocStyle, testthat, knitr, rmarkdown
Linking To Rcpp, Rhtslib, zlibbioc
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Follow Installation instructions to use this package in your R session.

Source Package Rfastp_1.14.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) Rfastp_1.14.0.tgz
macOS Binary (arm64) Rfastp_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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