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An R Wrapper for Bowtie2 and AdapterRemoval

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("Rbowtie2")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An Introduction to Rbowtie2 HTML R Script
Reference Manual PDF


biocViews Alignment, Preprocessing, Sequencing, Software
Version 2.10.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>= 3)
Depends R (>= 4.1.0)
Imports magrittr, Rsamtools
System Requirements C++11, GNU make, samtools
See More
Suggests knitr, testthat (>= 3.0.0), rmarkdown
Linking To
Depends On Me
Imports Me CircSeqAlignTk, esATAC, UMI4Cats, MetaScope
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package Rbowtie2_2.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) Rbowtie2_2.10.0.tgz
macOS Binary (arm64) Rbowtie2_2.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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