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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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Rbowtie

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 v1.3.0 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.

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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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