The high throughput of modern NGS sequencers coupled with the huge sizes of genomes currently analysed, poses always higher algorithmic challenges to align short reads quickly and accurately against a reference sequence. A crucial, additional, requirement is that the data structures used should be light. The available modern solutions usually are a compromise between the mentioned constraints: in particular, indexes based on the Burrows-Wheeler transform offer reduced memory requirements at the price of lower sensitivity, while hash-based text indexes guarantee high sensitivity at the price of significant memory consumption.

Fast randomized approximate string matching with succinct hash data structures / Policriti, Alberto; Prezza, Nicola. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 16 (Suppl 9):S4(2015), pp. 1-8. [10.1186/1471-2105-16-S9-S4]

Fast randomized approximate string matching with succinct hash data structures

PREZZA, Nicola
2015

Abstract

The high throughput of modern NGS sequencers coupled with the huge sizes of genomes currently analysed, poses always higher algorithmic challenges to align short reads quickly and accurately against a reference sequence. A crucial, additional, requirement is that the data structures used should be light. The available modern solutions usually are a compromise between the mentioned constraints: in particular, indexes based on the Burrows-Wheeler transform offer reduced memory requirements at the price of lower sensitivity, while hash-based text indexes guarantee high sensitivity at the price of significant memory consumption.
Sequence Analysis, DNA, Algorithms, Genome, hash, BWT
Fast randomized approximate string matching with succinct hash data structures / Policriti, Alberto; Prezza, Nicola. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 16 (Suppl 9):S4(2015), pp. 1-8. [10.1186/1471-2105-16-S9-S4]
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11385/192303
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