Supplementary material : large scale read classification for next generation sequencing

Hogan, James M. & Peut, Timothy (2014) Supplementary material : large scale read classification for next generation sequencing. International Conference on Computational Science. (In Press)


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: 69837
Item Type: Other
Refereed: No
Keywords: genomics , next generation sequencing , alignment free methods
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > BIOCHEMISTRY AND CELL BIOLOGY (060100) > Bioinformatics (060102)
Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > COMPUTER SOFTWARE (080300) > Bioinformatics Software (080301)
Divisions: Current > Schools > School of Electrical Engineering & Computer Science
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2014 The Author(s)
Deposited On: 06 Apr 2014 22:11
Last Modified: 06 Apr 2014 22:11

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