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Rfastp

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

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

DOI: 10.18129/B9.bioc.Rfastp

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] ORCID: 0000-0002-3216-7118 , Ji-Dung Luo [ctb] ORCID: 0000-0003-0150-1440 , Thomas Carroll [aut] ORCID: 0000-0002-0073-1714

Maintainer: Wei Wang <periwinkle.david at gmail.com>

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

Wei Wang, Thomas Carroll. Rfastp: An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing). doi:10.18129/B9.bioc.Rfastp, R package version 1.23.0, https://bioconductor.org/packages/Rfastp.

Generated from the package metadata; it may differ from the package's own citation.

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")

Details

Package Archives

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