RbowtieCuda

This is thereleased version of RbowtieCuda; for the devel version, seeRbowtieCuda.

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

DOI: 10.18129/B9.bioc.RbowtieCuda

Bioconductor version: Release (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], role = c("aut", "cre"))

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

Citation (from within R, entercitation("RbowtieCuda")):

Installation

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

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

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

Documentation

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

browseVignettes("RbowtieCuda")

An Introduction to RbowtieCuda	HTML	R Script
Reference Manual	PDF
NEWS	Text
INSTALL	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment,Coverage,Preprocessing,Sequencing,Software
Version	1.2.0
In Bioconductor since	BioC 3.21 (R-4.5) (0.5 years)
License	BSD_3_clause + fileLICENSE
Depends	R (>= 4.5.0)
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

Suggests	knitr,rmarkdown,RUnit,BiocGenerics
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	RbowtieCuda_1.2.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RbowtieCuda
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RbowtieCuda
Bioc Package Browser	https://code.bioconductor.org/browse/RbowtieCuda/
Package Short Url	https://bioconductor.org/packages/RbowtieCuda/
Package Downloads Report	Download Stats

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