MetaSim—A Sequencing Simulator for Genomics and Metagenomics

作者：Daniel C. Richter, Felix Ott, Alexander F. Auch, Ramona Schmid, Daniel H. Huson · 发表于：PLoS ONE · 年份：2008 · DOI：10.1371/journal.pone.0003373 · 被引用次数：485 · 研究领域：Genomics and Phylogenetic Studies、Genetics, Bioinformatics, and Biomedical Research、Microbial Community Ecology and Physiology

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.