Fast and accurate metagenomic short read analysis on GPUs

Metagenomics refers to the study of genomic sequences obtained directly from an environment. It is becoming increasingly popular due to the rapid advances in Next generation sequencing (NGS) technologies. NGS technologies generate vast amounts of data (DNA fragments or reads) so that input data set sizes are becoming increasingly bigger. The goal of this project is the design, implementation and evaluation of a new method for the classification of metagenomic reads whose accuracy is comparable to Mega-BLAST but whose speed is orders of magnitude faster. The speed advantage will be derived from algorithm design as well as efficient parallelization on CUDA-enabled GPUs.