Performance optimization in DNA short-read alignment.

ABSTRACT:

Summary

Over the past decade, short-read sequence alignment has become a mature technology. Optimized algorithms, careful software engineering and high-speed hardware have contributed to greatly increased throughput and accuracy. With these improvements, many opportunities for performance optimization have emerged. In this review, we examine three general-purpose short-read alignment tools-BWA-MEM, Bowtie 2 and Arioc-with a focus on performance optimization. We analyze the performance-related behavior of the algorithms and heuristics each tool implements, with the goal of arriving at practical methods of improving processing speed and accuracy. We indicate where an aligner's default behavior may result in suboptimal performance, explore the effects of computational constraints such

SUBMITTER: Wilton R 

PROVIDER: S-EPMC10060706 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature