CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment

Abstract

Next generation sequencing (NGS) technologies have enabled cheap, large-scale, and high-throughput production of short DNA sequence reads and thereby have promoted the explosive growth of data volume. Unfortunately, the produced reads are short and prone to contain errors that are incurred during sequencing cycles. Both large data volume and sequencing errors have complicated the mapping of NGS reads onto the reference genome and have motivated the development of various aligners for very short reads, typically less than 100 base pairs (bps) in length. As read length continues to increase, propelled by advances in NGS technologies, these longer reads tend to have higher sequencing error rates and more true mutations (including substitutions, insertions, or deletions) to the genome. Such new characteristics make inefficient the aligners, which are optimized for very short reads and support only ungapped alignments or gapped alignments with very limited number of gaps (typically one gap), and thereby call for new aligners with fully gapped alignment supported. In this chapter, we present the CUSHAW software suite for NGS read alignment, which is open-source and consists of three individual aligners: CUSHAW, CUSHAW2, and CUSHAW3. This suite offers parallel and efficient NGS read alignments to large genomes, such as the human genome, by harnessing multi-core CPUs or compute unified device architecture (CUDA)-enabled graphics processing units (GPUs). Moreover, it has the capability to align both base-space and color-space reads and is consistently shown to be one of the best alignment tools through our performance evaluations.