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.
The source code for bowtie v1.3.0 was obtained from 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.