Rfastp

DOI: 10.18129/B9.bioc.Rfastp    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date 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: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Rfastp
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Preprocessing, QualityControl, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-3 + file LICENSE
Depends
Imports	Rcpp, rjson, ggplot2, reshape2
LinkingTo	Rcpp, Rhtslib, zlibbioc
Suggests	BiocStyle, testthat, knitr, rmarkdown
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Rfastp_1.2.0.tar.gz
Windows Binary	Rfastp_1.2.0.zip
macOS 10.13 (High Sierra)	Rfastp_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rfastp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rfastp
Package Short Url	https://bioconductor.org/packages/Rfastp/
Package Downloads Report	Download Stats