May 24, 2016

Reference-free comparison of microbial communities via de Bruijn graphs

BioRxiv : the Preprint Server for Biology
Serghei Mangul, David Koslicki

Abstract

Microbial communities inhabiting the human body exhibit significant variability across different individuals and tissues, and are suggested to play an important role in health and disease. High-throughput sequencing offers unprecedented possibilities to profile microbial community composition, but limitations of existing taxonomic classification methods (including incompleteness of existing microbial reference databases) limits the ability to accurately compare microbial communities across different samples. In this paper, we present a method able to overcome these limitations by circumventing the classification step and directly using the sequencing data to compare microbial communities. The proposed method provides a powerful reference-free way to assess differences in microbial abundances across samples. This method, called EMDeBruijn, condenses the sequencing data into a de Bruijn graph. The Earth Mover's Distance (EMD) is then used to measure similarities and differences of the microbial communities associated with the individual graphs. We apply this method to RNA-Seq data sets from a coronary artery calcification (CAC) study and shown that EMDeBruijn is able to differentiate between case and control CAC samples while uti...Continue Reading

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Mentioned in this Paper

Study
CAC Codon-amino Acid Adaptor Activity
Classification
TPRG1L gene
Nucleic Acid Sequencing
Sequencing
Microbial
High-Throughput RNA Sequencing
Human Body Structure
Electromechanical Dissociation

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