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SEK: sparsity exploiting k-mer-based estimation of bacterial community composition Public Deposited

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https://ir.library.oregonstate.edu/concern/articles/9w032773t

This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version, Chatterjee, S., Koslicki, D., Dong, S., Innocenti, N., Cheng, L., Lan, Y., ... & Corander, J. (2014). SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition. Bioinformatics, 30(17), 2423-2431. doi:10.1093/bioinformatics/btu320, is available online at:  http://bioinformatics.oxfordjournals.org/content/30/17/2423. The published article is copyrighted by the Author(s) and published by Oxford University Press.

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  • MOTIVATION: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. Since the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically very time consuming in a desktop computing environment. RESULTS: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method which is shown to be more robust to input data variation than a recently introduced related method. AVAILABILITY: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above website.
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  • Chatterjee, S., Koslicki, D., Dong, S., Innocenti, N., Cheng, L., Lan, Y., ... & Corander, J. (2014). SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition. Bioinformatics, 30(17), 2423-2431. doi:10.1093/bioinformatics/btu320
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  • 30
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  • 17
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  • Erasmus Mundus scholar program of the EuropeanUnion (Y.L.), by the Academy of Finland through its FinlandDistinguished Professor program grant project 129024/Aurell (toE.A.), ERC grant 239784 (to J.C.) and the Academy of FinlandCenter of Excellence COIN (to E.A. and J.C.), by the SwedishResearch Council Linnaeus Centre ACCESS (to E.A., M.S.,L.R., S.C. and M.V) and by the Ohio Supercomputer Centerand the Mathematical Biosciences Institute at The Ohio StateUniversity (to D.K.).
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