The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
MetaSim—A Sequencing Simulator for Genomics and Metagenomics
Open accessAbstract
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.
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Cites
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Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
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Cited by
metaSPAdes: a new versatile metagenomic assembler
Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496
Wooley, J. C., Godzik, A., & Friedberg, I. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000667 · Cited by 688
Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim
Balzer, S., Malde, K., Lanzén, A., Sharma, A., & Jonassen, I. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq365 · Cited by 124
Metadata
- Authors
- Richter, D. C., Ott, F., Auch, A. F., Schmid, R., & Huson, D. H.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2008-10-08
- Volume
- 3
- Issue
- 10
- Pages
- e3373
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2048818637
- Cited by
- 464
- References
- 6
- FWCI
- 10.67
- Type
- journal article
- Language
- en
- Open access
- gold
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- Richter, D. C., Ott, F., Auch, A. F., Schmid, R., & Huson, D. H. (2008). MetaSim—A Sequencing Simulator for Genomics and Metagenomics. PLoS ONE. https://doi.org/10.1371/journal.pone.0003373
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