Nature Methods
- 4, 495 - 500 (2007)
Published online: 29 April 2007; | doi:10.1038/nmeth1043
Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsKonstantinos Mavromatis1, Natalia Ivanova1, Kerrie Barry1, Harris Shapiro1, Eugene Goltsman1, Alice C McHardy2, Isidore Rigoutsos2, Asaf Salamov1, Frank Korzeniewski1, Miriam Land3, Alla Lapidus1, Igor Grigoriev1, Paul Richardson1, Philip Hugenholtz1 & Nikos C Kyrpides11
Department of Energy Joint Genome Institute (DOE-JGI), 2800 Mitchell Drive, Walnut Creek, California
94598, USA. 2
Bioinformatics and Pattern Discovery Group, IBM T.J. Watson Research Center, 1101 Kitchawan Rd., Yorktown Heights, New York
10598, USA. 3
Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, USA.
Correspondence should be addressed to Konstantinos Mavromatis kmavrommatis@lbl.gov 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 ARTICLES LIKE THIS These links to content published by NPG are automatically generated.
|
