NVBIO

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA. Though it is specifically designed to unleash the power of NVIDIA GPUs, most of its components are completely cross-platform and can be used both from host C++ and device CUDA code.

Introduction

• Generic Programming
• Host & Device
• Hello DNA!
• Hello DNA! - Part 2
• All-Mapping using an FM-index
• Protein Search using Wavelet Trees and an FM-index
• Smith-Waterman Alignment of Protein Strings

Modules

NVBIO includes the following modules:

• Basic Module
• Strings Module
• Alignment Module
• FM-Index Module
• Q-Gram Module
• Sufsort Module
• Tries Module
• I/O Module
• FASTA Parsers
• FASTQ Parsers

Performance

NVBIO is designed for performance. Here's a couple benchmarks showing the superior speed of its FM-index search, DP alignment and BWT construction algorithms.

Dependencies

NVBIO depends on the following external libraries:

• CUB
• SAIS
• zlib
• crc
• a modification of Nathaniel McClatchey's priority_deque

Licensing

NVBIO has been developed by NVIDIA Corporation and is licensed under BSD.

Contributors

The main contributors of NVBIO are Jacopo Pantaleoni and Nuno Subtil.