Use of simulated data sets to evaluate the fidelity of metagenomic processing methods View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-04-29

AUTHORS

Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice C McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Paul Richardson, Philip Hugenholtz, Nikos C Kyrpides

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.Please visit methagora to view and post comments on this article More... »

PAGES

495-500

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth1043

DOI

http://dx.doi.org/10.1038/nmeth1043

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1047202519

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17468765


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62 processing methods
63 processing steps
64 reads
65 real metagenomes
66 research
67 sequence
68 set
69 simulated data sets
70 standardized benchmarking
71 step
72 structure
73 terms
74 terms of complexity
75 tool
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