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
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.