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 (3.24)
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 [cre, aut]
, Ji-Dung Luo [ctb]
, Thomas Carroll [aut]
Maintainer: Wei Wang <periwinkle.david at gmail.com>
citation("Rfastp")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 |
| 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | Rfastp_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | Rfastp_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | Rfastp_1.23.0.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 |