Rbowtie2

DOI: 10.18129/B9.bioc.Rbowtie2    

An R Wrapper for Bowtie2 and AdapterRemoval

Bioconductor version: Release (3.14)

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.

Author: Zheng Wei [aut, cre], Wei Zhang [aut]

Maintainer: Zheng Wei <wzweizheng at qq.com>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rbowtie2")

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("Rbowtie2")

 

HTML	R Script	An Introduction to Rbowtie2
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Preprocessing, Sequencing, Software
Version	2.0.0
In Bioconductor since	BioC 3.6 (R-3.4) (4.5 years)
License	GPL (>= 3)
Depends	R (>= 4.1.0)
Imports	magrittr, Rsamtools
LinkingTo
Suggests	knitr, testthat (>= 3.0.0), rmarkdown
SystemRequirements	C++11, GNU make, samtools
Enhances
URL
Depends On Me
Imports Me	esATAC, UMI4Cats
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Rbowtie2_2.0.0.tar.gz
Windows Binary	Rbowtie2_2.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	Rbowtie2_2.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rbowtie2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rbowtie2
Package Short Url	https://bioconductor.org/packages/Rbowtie2/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive