An alignment-free method for profiling microbial community

Abstract

Determining abundances of microbial genomes in metagenomic samples is an important problem in analyzing metagenomic data. Homology-based method requires aligning reads from metagenomic samples to reference genomes and can be a computationally expensive as microbial communities usually consists of hundreds to thousands of environmental microbial species. We introduce an efficient alignment-free approach to estimate abundances of microbial genomes in metagenomic samples. The approach is based on solving linear and quadratic programs, which are represented by genome-specific markers. In a controlled study at different levels of contamination, our method was able to achieve higher accuracy compared to current composition-based methods in estimating abundances of microbial genomes.

Publication Title

Proceedings of the 8th International Conference on Bioinformatics and Computational Biology, BICOB 2016

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