An Ultra-fast Approach to Align Longer Short Reads onto Human Genome

With the advent of second-generation sequencing (SGS) technologies, deoxyribonucleic acid (DNA) sequencing machines have started to produce reads, named as “longer short reads”, which are much longer than previous generation reads, the so called “short reads”. Unfortunately, most of the existing read aligners do not scale well for those second-generation longer short reads. Moreover, many of the existing aligners are limited only to the short reads of previous generation. In this paper, we have proposed a new approach to solve this essential read alignment problem for current generation longer short reads. Our ultra-fast approach uses a hash-based indexing and searching scheme to find exact matching for second-generation longer short reads within reference genome. The experimental study shows that the proposed ultra-fast approach can accurately find matching of millions of reads against human genome within few seconds and it is an order of magnitude faster than Burrows-Wheeler Transform (BWT) based methods such as BowTie and Burrows-Wheeler Aligner (BWA) for a wide range of read length.