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PLoS One. 2008 Oct 8;3(10):e3373. doi: 10.1371/journal.pone.0003373.

MetaSim: a sequencing simulator for genomics and metagenomics.

Author information

1
ZBIT- Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany. drichter@informatik.uni-tuebingen.de

Abstract

BACKGROUND:

The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets.

METHODOLOGY/PRINCIPAL FINDINGS:

To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree.

CONCLUSIONS/SIGNIFICANCE:

MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.

PMID:
18841204
PMCID:
PMC2556396
DOI:
10.1371/journal.pone.0003373
[Indexed for MEDLINE]
Free PMC Article

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