Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

Synonyms

Genome Relative Abundance estimation using Mixture Model theory (GRAMMy)

Introduction

Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomic analysis. However, it is also a challenging computational problem because of the mixed nature of metagenomes and the fact that only a small fraction of them get sequenced.

With the advents of next-generation sequencing (NGS) technologies, there has been significant increase in sequencing capacity yet reduction in single read length. This paradigm shift in sequencing technologies has impacted downstream analyses. Specifically, the identification of the origin of a read becomes more difficult for several reasons. First, a large number of short reads cannot be uniquely mapped to a specific location of one genome. Instead, they map to multiple locations of one or multiple genomes. These ambiguities are directly associated with the read length reduction in NGS...