Rbowtie-package {Rbowtie} | R Documentation

## R bowtie wrapper

### Description

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 QuasR instead of using `Rbowtie` directly. QuasR provides a simpler interface than `Rbowtie` and covers the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification.

We also recommend to use Rhisat2 instead of SpliceMap for spliced alignment, which provides a more up-to-date and improved spliced short read aligner.

### Author(s)

Florian Hahne, Anita Lerch, Michael B Stadler

### References

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3):R25 (2009).

Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research, 38(14):4570-8 (2010).

### See Also

`bowtie`, `SpliceMap`

[Package Rbowtie version 1.34.0 Index]