Rfastp

This is the development version of Rfastp; for the stable release version, see Rfastp.

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

Bioconductor version: Development (3.21)

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] (ORCID: ), Ji-Dung Luo [ctb] (ORCID: ), Thomas Carroll [cre, aut] (ORCID: )

Maintainer: Thomas Carroll <tc.infomatics at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Preprocessing, QualityControl, Sequencing, Software
Version	1.17.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
License	GPL-3 + file LICENSE
Depends
Imports	Rcpp, rjson, ggplot2, reshape2
System Requirements	GNU make
URL

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_1.17.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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