Occupancy Modeling, Maximum Contig Size Probabilities and Designing Metagenomics Experiments

Stephen A Stanhope,Iddo Friedberg

doi:10.1371/journal.pone.0011652

Abstract

Mathematical aspects of coverage and gaps in genome assembly have received substantial attention by bioinformaticians. Typical problems under consideration suppose that reads can be experimentally obtained from a single genome and that the number of reads will be set to cover a large percentage of that genome at a desired depth. In metagenomics experiments genomes from multiple species are simultaneously analyzed and obtaining large numbers of reads per genome is unlikely. We propose the probability of obtaining at least one contig of a desired minimum size from each novel genome in the pool without restriction based on depth of coverage as a metric for metagenomic experimental design. We derive an approximation to the distribution of maximum contig size for single genome assemblies using relatively few reads. This approximation is verified in simulation studies and applied to a number of different metagenomic experimental design problems, ranging in difficulty from detecting a single novel genome in a pool of known species to detecting each of a random number of novel genomes collectively sized and with abundances corresponding to given distributions in a single pool.

Highlights

Recent experiments in metagenomics have proposed that genetic sequences from previously uncatagologued species can be discovered/recovered and investigated by subjecting large samples of RNA or DNA taken from a pool of organisms representative of a set of different species to shotgun sequencing and assembly [1,2,3,4,5,6,7]
Large samples of genomic material from organisms representing a number of different species are simultaneously sequenced and assembled
Such analyses have some similarities to more typical sequencing experiments in which a single genome is studied in isolation, the change in problem context justifies an evaluation of the body of analytical and computational technique that has been developed for single organism problems, and where appropriate the development of new tools

Summary

Introduction

Recent experiments in metagenomics ( known as community genomics or environmental genomics) have proposed that genetic sequences from previously uncatagologued species can be discovered/recovered and investigated by subjecting large samples of RNA or DNA taken from a pool of organisms representative of a set of different species to shotgun sequencing and assembly [1,2,3,4,5,6,7]. In an early project viruses isolated from seawater samples were lysed and the recovered DNA molecules were sequenced and assembled, yielding contigs from a number of previously unsequenced virus species [11] This was followed by a number of additional sea and ocean water analyses that investigated issues relating to microbial diversity, phylogeny, structure and function [12,13,14,15]. It can be anticipated that further human studies will continue to be proposed and performed

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