DOI: 10.18129/B9.bioc.Rbowtie    

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

R bowtie wrapper

Bioconductor version: Development (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, Anita Lerch, Michael B Stadler

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))

# The following initializes usage of Bioc devel


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


biocViews Alignment, Sequencing, Software
Version 1.39.0
In Bioconductor since BioC 2.12 (R-3.0) (9.5 years)
License Artistic-2.0 | file LICENSE
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
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_1.39.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/Rbowtie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rbowtie
Package Short Url https://bioconductor.org/packages/Rbowtie/
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