## Rbowtie The `Rbowtie` R package provides an R interface to the [`bowtie`](http://bowtie-bio.sourceforge.net/index.shtml) short-read aligner by [Langmead et al. (2009)](http://genomebiology.com/2009/10/3/R25), as well as to [`SpliceMap`](https://web.stanford.edu/group/wonglab/SpliceMap/) by [Au et al. (2010)](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq211). 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`](https://bioconductor.org/packages/QuasR/) bioconductor package. We recommend to use the `QuasR` package instead of using `Rbowtie` directly. ### Source code The source code for bowtie v1.3.0 was obtained from [https://github.com/BenLangmead/bowtie/archive/v1.3.0.tar.gz](https://github.com/BenLangmead/bowtie/archive/v1.3.0.tar.gz) on November 2, 2020. 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 | |:----------------:|:----------------:|:----------------:|:----------------:| | GitHub Actions | Linux/Windows/macOS | [](https://github.com/fmicompbio/Rbowtie/actions) | [](https://codecov.io/github/fmicompbio/Rbowtie) | | Bioc ([_devel_](http://bioconductor.org/packages/devel/bioc/html/Rbowtie.html)) | Multiple | [](http://bioconductor.org/checkResults/devel/bioc-LATEST/Rbowtie) | [](https://codecov.io/github/fmicompbio/Rbowtie) | | Bioc ([_release_](http://bioconductor.org/packages/release/bioc/html/Rbowtie.html)) | Multiple | [](http://bioconductor.org/checkResults/release/bioc-LATEST/Rbowtie) | [](https://codecov.io/github/fmicompbio/Rbowtie) |