Rfastp
This package is for version 3.16 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: 3.16
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 "4.2") 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 | ||
| LICENSE | Text |
Details
| biocViews | Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary | Rfastp_1.8.0.zip |
| macOS Binary (x86_64) | Rfastp_1.8.0.tgz |
| macOS Binary (arm64) | Rfastp_1.8.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |