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 (3.20)
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("Rfastp")
):
Installation
To install this package, start R (version "4.4") 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 | ||
LICENSE | Text |
Details
biocViews | Preprocessing, QualityControl, Sequencing, Software |
Version | 1.15.0 |
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 |
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_1.15.0.tar.gz |
Windows Binary (x86_64) | Rfastp_1.15.0.zip |
macOS Binary (x86_64) | Rfastp_1.15.0.tgz |
macOS Binary (arm64) | Rfastp_1.15.0.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 |