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
AuthorsTárraga J, Arnau V, Martínez H, Moreno R, Cazorla D, Salavert-Torres J, Blanquer-Espert I, Dopazo J, Medina I
Journal TitleBioinformatics (Oxford, England)
Volume30
Pages3396-3398
Journal Date2014 Aug 20
ISSN1367-4811
KeywordsNGS, short read mapping. HPC. suffix arrays
AbstractHPG 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 20x 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.
URLhttp://bioinformatics.oxfordjournals.org/content/early/2014/08/19/bioinformatics.btu553.long
DOI10.1093/bioinformatics/btu553
Alternate JournalBioinformatics