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2014 (English)In: Bioinformatics, ISSN 1460-2059, Vol. 30, no 17, p. 2423-2431Article in journal (Refereed) Published
Abstract [en]
Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As 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 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 and implementation: 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 Web site.
Place, publisher, year, edition, pages
Oxford University Press, 2014
Keywords
bacterial community composition, sparsity, metagenomics
National Category
Bioinformatics (Computational Biology)
Research subject
Computer Science
Identifiers
urn:nbn:se:kth:diva-152814 (URN)10.1093/bioinformatics/btu320 (DOI)000342912400046 ()24812337 (PubMedID)2-s2.0-84907029456 (Scopus ID)
Funder
Swedish Research Council
Note
QC 20141023
2014-10-012014-10-012024-03-18Bibliographically approved