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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.
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README.md

Rbowtie

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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 v1.2.2_p1 was obtained from https://github.com/BenLangmead/bowtie/archive/v1.2.2_p1.tar.gz on March 13, 2019, and patched to include additional changes available on github since the release (up to master branch commit 58c6ac9 from Sep 5, 2018, and additional unmerged pull request #74, commit c7004c790a73cd34a0e5dffcb31d7c184d3e7250). The folders genomes, reads, doc, indexes and scripts were not included into the package to reduce its size.

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