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Rfastp

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


Bioconductor version: Release (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rfastp")

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

Documentation

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

browseVignettes("Rfastp")
Rfastp HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Preprocessing, QualityControl, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3 + file LICENSE
Depends
Imports Rcpp, rjson, ggplot2, reshape2
System Requirements GNU make
URL
See More
Suggests BiocStyle, testthat, knitr, rmarkdown
Linking To Rcpp, Rhtslib, zlibbioc
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Rfastp_1.12.0.tar.gz
Windows Binary Rfastp_1.12.0.zip
macOS Binary (x86_64) Rfastp_1.12.0.tgz
macOS Binary (arm64) Rfastp_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rfastp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rfastp
Bioc Package Browser https://code.bioconductor.org/browse/Rfastp/
Package Short Url https://bioconductor.org/packages/Rfastp/
Package Downloads Report Download Stats