Sequence alignment tools: one parallel pattern to rule them all?
In this paper, we advocate high-level programming methodology for next generation sequencers (NGS) alignment tools for both productivity and absolute performance. We analyse the problem of parallel alignment and review the parallelisation strategies of the most popular alignment tools, which can all...
| Publicado en: | BioMed Research International Vol. 2014; pp. 539410 - 539411 |
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| Autores principales: | , , , |
| Formato: | Journal Article |
| Publicado: |
Wiley-Blackwell
2014
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=109676237&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 109676237 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 2014 vid: 2014 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 109676237 NLM25147803 2012693268 10.1155/2014/539410 NLM25147803 PMC4131566 109676237 ppf: 539410 ppct: 1 formats: fmt: @attributes: type: P tig: atl: Sequence alignment tools: one parallel pattern to rule them all? aug: au: Misale, Claudia Ferrero, Giulio Torquati, Massimo Aldinucci, Marco sug: ab: In this paper, we advocate high-level programming methodology for next generation sequencers (NGS) alignment tools for both productivity and absolute performance. We analyse the problem of parallel alignment and review the parallelisation strategies of the most popular alignment tools, which can all be abstracted to a single parallel paradigm. We compare these tools to their porting onto the FastFlow pattern-based programming framework, which provides programmers with high-level parallel patterns. By using a high-level approach, programmers are liberated from all complex aspects of parallel programming, such as synchronisation protocols, and task scheduling, gaining more possibility for seamless performance tuning. In this work, we show some use cases in which, by using a high-level approach for parallelising NGS tools, it is possible to obtain comparable or even better absolute performance for all used datasets. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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