Large scale read classification for next generation sequencing

Hogan, James M. & Peut, Timothy (2014) Large scale read classification for next generation sequencing. Procedia Computer Science, 29, pp. 2003-2012.

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Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.

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ID Code: 74424
Item Type: Journal Article
Refereed: Yes
Additional Information: Proceedings of 2014 International Conference on Computational Science
Keywords: Genomics, Next generation, Sequencing, Alignment-free methods, Machine learning
DOI: 10.1016/j.procs.2014.05.184
ISSN: 1877-0509
Divisions: Current > Schools > School of Electrical Engineering & Computer Science
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2014 Elsevier B.V.
Deposited On: 27 Jul 2014 23:20
Last Modified: 11 Aug 2014 02:58

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