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RbowtieCuda package: an R wrapper for nvBowtie, a fork version of the NVBIO library.

The RbowtieCuda package provides an R interface to nvBowtie1, a CUDA-based adaptation of the popular Bowtie2 short-read aligner, originally developed by Jacopo Pantaleoni and collaborators. This package allows users to build genome indexes and create alignment files in .sam or .bam formats, leveraging the computational power of modern NVIDIA GPUs for significantly faster processing speeds. nvBowtie is part of the NVBIO library, and the package also includes an experimental implementation of the Wavefront Alignment (WFA) method 2.

Source Package Information

The RbowtieCuda is built on a modified version of the nvBIO v1.1.50 source code, which can be accessed at https://github.com/NVlabs/nvbio.

Acknowledgements

We would like to thank Ismael Galve Roperh for his assistance.

Contributors

Original NVBIO developers:

Jacopo Pantaleoni - jpantaleoni@nvidia.com
Nuno Subtil - nsubtil@nvidia.com

RbowtieCuda developers:

Samuel Simon Sanchez - samsimon@ucm.es
Franck RICHARD - franck.richard@winstars.net

Maintainer: Franck RICHARD

References

[1] Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.

[2] Marco-Sola S, Moure JC, Moreto M et al. Fast gap-affine pairwise alignment using the wavefront algorithm. Bioinformatics 2021;37: 456–63.