MetaSim

Application data
Biological application domain(s)	Metagenomics, Genomics
Principal bioinformatics method(s)	Simulation, Assembly, Mapping
Maintained?	Maybe
Programming language(s)	Java
Licence	Free for academic use

Summary: 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. The resulting data sets can be used as standardized test scenarios for planning sequencing projects or for benchmarking assembler and metagenomic software.

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References

1. . 2008. PLoS One

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