DOI: 10.18129/B9.bioc.Rbowtie  

R bowtie wrapper

Bioconductor version: Release (3.17)

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Author: Florian Hahne [aut], Anita Lerch [aut], Michael Stadler [aut, cre]

Maintainer: Michael Stadler <michael.stadler at fmi.ch>

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


To install this package, start R (version "4.3") 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:



HTML R Script An introduction to Rbowtie
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Sequencing, Software
Version 1.40.0
In Bioconductor since BioC 2.12 (R-3.0) (10.5 years)
License Artistic-2.0 | file LICENSE
Imports utils
Suggests testthat, parallel, BiocStyle, knitr, rmarkdown
SystemRequirements GNU make
URL https://github.com/fmicompbio/Rbowtie
BugReports https://github.com/fmicompbio/Rbowtie/issues
Depends On Me QuasR
Imports Me crisprBowtie, multicrispr, seqpac
Suggests Me crisprDesign, eisaR
Links To Me
Build Report  

Package Archives

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

Source Package Rbowtie_1.40.0.tar.gz
Windows Binary Rbowtie_1.40.0.zip (64-bit only)
macOS Binary (x86_64) Rbowtie_1.40.0.tgz
macOS Binary (arm64) Rbowtie_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rbowtie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rbowtie
Bioc Package Browser https://code.bioconductor.org/browse/Rbowtie/
Package Short Url https://bioconductor.org/packages/Rbowtie/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive

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