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Bioconductor - RbowtieCuda (development version)

RbowtieCuda

This is the development version of RbowtieCuda; for the stable release version, see RbowtieCuda.

An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda

Bioconductor version: Development (3.22)

This package provides an R wrapper for the popular Bowtie2 sequencing read aligner, optimized to run on NVIDIA graphics cards. It includes wrapper functions that enable both genome indexing and alignment to the generated indexes, ensuring high performance and ease of use within the R environment.

Author: c(Jacopo Pantaleoni [aut], Nuno Subtil [aut], Samuel Simon Sanchez [aut], Franck RICHARD [aut, cre])

Maintainer: Franck RICHARD <franck.richard at winstars.net>

Citation (from within R, enter citation("RbowtieCuda")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RbowtieCuda")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RbowtieCuda")
Details biocViews Alignment, Coverage, Preprocessing, Sequencing, Software Version 1.1.1 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License BSD_3_clause + file LICENSE Depends R (>= 4.4.0) Imports methods System Requirements C++20, GNU make, cmake, CUDA Toolkit(>=10), MSVC, libthrust-dev, libcub-dev, gcc, g++ URL https://github.com/FranckRICHARD01/RbowtieCuda https://belacqua-labo.ovh/bioinformatic/RbowtieCuda Bug Reports https://github.com/FranckRICHARD01/RbowtieCuda/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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