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

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.

SUBMITTER: Tarraga J

PROVIDER: S-EPMC4816028 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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

Tárraga Joaquín J Arnau Vicente V Martínez Héctor H Moreno Raul R Cazorla Diego D Salavert-Torres José J Blanquer-Espert Ignacio I Dopazo Joaquín J Medina Ignacio I

Bioinformatics (Oxford, England) 20140820 23

<h4>Unlabelled</h4>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 ...[more]

PMID: 25143289

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