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MUMmerGPU: High-throughput sequence alignment using Graphics Processing Units

Abstract

The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies.

Traditionally, Graphics Processing Units (GPUs) have been highly specialized with two distinct classes of graphics stream processors: vertex processors, which compute geometric transformations on meshes, and fragment processors, which shade and illuminate the rasterized products of the vertex processors. Modern GPUs include several processors (tens to hundreds) of each type, and are organized in a streaming, data-parallel model in which the processors execute the same instructions on multiple data streams simultaneously. As GPUs have become increasingly more powerful and ubiquitous, though, researchers have begun using its power for non-graphics, or general-purpose (GPGPU) applications.

MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in replacement for MUMmer, using the GPUs in common workstations to simultaneously align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies.