ARK : Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

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Koslicki , D , Chatterjee , S , Shahrivar , D , Walker , A W , Francis , S C , Fraser , L J , Vehkaperae , M , Lan , Y & Corander , J 2015 , ' ARK : Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition ' , PLoS One , vol. 10 , no. 10 , 0140644 .

Title: ARK : Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition
Author: Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W.; Francis, Suzanna C.; Fraser, Louise J.; Vehkaperae, Mikko; Lan, Yueheng; Corander, Jukka
Other contributor: University of Helsinki, Department of Mathematics and Statistics

Date: 2015-10-23
Language: eng
Number of pages: 16
Belongs to series: PLoS One
ISSN: 1932-6203
Abstract: Motivation Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. Results There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. Availability An open source, platform-independent implementation of the method in the Julia programming language is freely available at A Matlab implementation is available at
112 Statistics and probability

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