The Rbowtie R package provides an R interface to the bowtie short-read aligner by Langmead et al. (2009), as well as to SpliceMap by Au et al. (2010). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index. These are used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Source code

The source code for bowtie v1.2.3 was obtained from on December 13, 2019. The folders genomes, reads, doc, indexes and scripts were not included into the package to reduce its size.

Software status

| Platforms | OS | R CMD check | Coverage | |:----------------:|:----------------:|:----------------:|:----------------:| | Travis CI | Linux | Travis CI build status | coverage status | | Appveyor | Windows | Build status (Windows) | coverage status | | GitHub Actions | Linux/Windows/macOS | R build status | coverage status | | Bioc (devel) | Multiple | Bioconductor-devel Build Status | coverage status | | Bioc (release) | Multiple | Bioconductor-release Build Status | coverage status |

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Rbowtie documentation built on Nov. 8, 2020, 6:11 p.m.