Reconstructing genomes of organisms from high-throughput sequencing experiments without a reference genome available (de novo assembly) is a challenging problem which has been approached in several ways in the past decade. Although numerous methods are available and many offer fair performance in reconstruction, there is a lack of generalized template libraries and interchangeable data structures/methods for serial, multithreaded and distributed processing. In this work we propose a novel set of cache oblivious generic data structures for serial, multithreaded and distributed processing of high-throughput sequencing data for the creation of de Bruijn or k-mer graphs towards their usage in de novo assembly and related HTS data analytics problems.

Milicchio, F. (2016). High-performance data structures for de novo assembly of genomes: cache oblivious generic programming. In Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics [10.1145/2975167.2985691].

High-performance data structures for de novo assembly of genomes: cache oblivious generic programming

MILICCHIO, Franco
2016

Abstract

Reconstructing genomes of organisms from high-throughput sequencing experiments without a reference genome available (de novo assembly) is a challenging problem which has been approached in several ways in the past decade. Although numerous methods are available and many offer fair performance in reconstruction, there is a lack of generalized template libraries and interchangeable data structures/methods for serial, multithreaded and distributed processing. In this work we propose a novel set of cache oblivious generic data structures for serial, multithreaded and distributed processing of high-throughput sequencing data for the creation of de Bruijn or k-mer graphs towards their usage in de novo assembly and related HTS data analytics problems.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11590/320473
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