RbowtieCuda

RbowtieCuda wraps the nvBowtie and nvBWT rewritten version of Bowtie2, enabling GPU-accelerated genome indexing and read alignment on NVIDIA graphics cards within the R environment.

Key Features:

• GPU-accelerated alignment: Leverages NVIDIA CUDA graphics cards to run the Bowtie2 alignment algorithm with substantially improved performance.
• Genome indexing: Provides wrapper functions for generating genome indexes using the nvBWT indexing component.
• Read alignment: Enables alignment of sequencing reads to generated indexes using nvBowtie.
• R integration: Functions operate natively within the R environment for bioinformatics workflows.

Scientific Applications:

• High-throughput sequencing analysis: Accelerates alignment of large-scale next-generation sequencing datasets using GPU hardware.
• Genomic read mapping: Maps DNA sequencing reads to reference genomes for downstream variant calling, expression analysis, and other genomic studies.

Methodology:

The package provides R wrapper functions that interface with nvBowtie and nvBWT, rewritten CUDA implementations of the Bowtie2 aligner and its Burrows-Wheeler transform indexer.