title: Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
abstract: Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based (blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.
authors.affiliation: Department of Energy Joint Genome Institute (DOE-JGI), 2800 Mitchell Drive, Walnut Creek, California 94598, USA. kmavrommatis@lbl.gov
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.forename: Harris
authors.initials: H
authors.lastname: Shapiro
authors.forename: Eugene
authors.initials: E
authors.lastname: Goltsman
authors.forename: Alice C
authors.initials: AC
authors.lastname: McHardy
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Frank
authors.initials: F
authors.lastname: Korzeniewski
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Igor
authors.initials: I
authors.lastname: Grigoriev
authors.forename: Paul
authors.initials: P
authors.lastname: Richardson
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D003198:Computer Simulation; D030541:Databases, Genetic; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods* / Q000592:standards; D010802:Phylogeny; D012984:Software