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EnglishThe 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:Suppl 9(2015), p. S4.
| Titolo: | Fast randomized approximate string matching with succinct hash data structures |
| Autori: | |
| Data di pubblicazione: | 2015 |
| Rivista: | |
| Citazione: | Fast randomized approximate string matching with succinct hash data structures / Policriti, Alberto; Prezza, Nicola. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 16 Suppl 9:Suppl 9(2015), p. S4. |
| 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. |
| Handle: | http://hdl.handle.net/11390/1068702 |
| Appare nelle tipologie: | 1.1 Articolo in rivista |
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