YOABS: yet other aligner of biological sequences—an efficient linearly scaling nucleotide aligner

摘要

Motivation: Explosive growth of short-read sequencing technologies in the recent years resulted in rapid development of many new alignment algorithms and programs. But most of them are not efficient or not applicable for reads ≳200 bp because these algorithms specifically designed to process short queries with relatively low sequencing error rates. However, the current trend to increase reliability of detection of structural variations in assembled genomes as well as to facilitate de novo sequencing demand complimenting high-throughput short-read platforms with long-read mapping. Thus, algorithms and programs for efficient mapping of longer reads are becoming crucial. However, the choice of long-read aligners effective in terms of both performance and memory are limited and includes only handful of hash table (BLAT, SSAHA2) or trie (Burrows-Wheeler Transform - Smith-Waterman (BWT-SW), Burrows-Wheeler Alignerr - Smith-Waterman (BWA-SW)) based algorithms.