Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.

TitleAcceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Publication TypeJournal Article
Year of Publication2014
AuthorsTarraga J, Arnau V, Martínez H, Moreno R, Cazorla D, Salavert-Torres J, Blanquer-Espert I, Dopazo J, Medina I
JournalBioinformatics
Volume30
Pagination3396-8
Date Published2014 Dec 1
ISSN1367-4811
KeywordsAlgorithms, Animals, DNA, Drosophila, High-Throughput Nucleotide Sequencing, Humans, Sequence Alignment, Sequence Analysis, Software
Abstract

UNLABELLED: HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20× for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.AVAILABILITY AND IMPLEMENTATION: https://github.com/opencb/hpg-aligner.

DOI10.1093/bioinformatics/btu553