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Accurate high throughput alignment via line sweep-based seed processing

Title
Accurate high throughput alignment via line sweep-based seed processing
Author
Heese, Klaus
Keywords
CHAINING ALGORITHMS; SEQUENCE; SEARCH; VERSATILE; READS
Issue Date
2019-04
Publisher
NATURE PUBLISHING GROUP
Citation
NATURE COMMUNICATIONS, v. 10, no. 1939
Abstract
Accurate and fast aligners are required to handle the steadily increasing volume of sequencing data. Here we present an approach allowing performant alignments of short reads (Illumina) as well as long reads (Pacific Bioscience, Ultralong Oxford Nanopore), while achieving high accuracy, based on a universal three-stage scheme. It is also suitable for the discovery of insertions and deletions that originate from structural variants. We comprehensively compare our approach to other state-of-the-art aligners in order to confirm its performance with respect to accuracy and runtime. As part of our algorithmic scheme, we introduce two line sweep-based techniques called "strip of consideration" and "seed harmonization". These techniques represent a replacement for chaining and do not rely on any specially tailored data structures. Additionally, we propose a refined form of seeding on the foundation of the FMD-index.
URI
https://www.nature.com/articles/s41467-019-09977-2http://repository.hanyang.ac.kr/handle/20.500.11754/110646
ISSN
2041-1723
DOI
10.1038/s41467-019-09977-2
Appears in Collections:
GRADUATE SCHOOL OF BIOMEDICAL SCIENCE AND ENGINEERING[S](의생명공학전문대학원) > ETC
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