Bioconductor package: an R wrapper for mvBowtie, a fork version of NVBIO.
The RbowtieCuda package provides an R interface to the nvBowtie[1] short read aligner adaptation of bowtie2 unning under Cuda proposed by Jacopo Pantaleoni and al. The RbowtiCuda package allows users to build indexes and to create alignment files (.sam or .bam) but with a higher processing speed thanks to the computing power of modern video cards. nvBowtie is a part of the NVBIO library.
The RbowtieCuda package uses a modificated version of the nvBio v1.1.50 source code which was obtained from https://github.com/NVlabs/nvbio.
We would like to thank Ismael Galve Roperh for his assistance.
The main contributors of the original NVBIO are:
Jacopo Pantaleoni - [email protected]
Nuno Subtil - [email protected]
RbowtieCuda developers:
Samuel Simon Sanchez - [email protected]
Franck RICHARD - [email protected]
The maintainer of the RbowtieCuda package is Franck RICHARD
[1] Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.