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MetaSim Description

A Sequencing Simulator for Genomics and Metagenomics

The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing an 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. To facilitate the development and improvement of metagenomic tools, 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.
The resulting data sets can be used as standardized test scenarios for planning sequencing projects or for benchmarking assembler and metagenomic software.

Feature List:

MetaSim

* integrates a database for source genome sequences
* generates sets of synthetic reads or mate-pairs based on adaptable sequencing error models (e.g. for Sanger chemistry, Roche's 454 and Illumina (former Solexa)
* enables the user to configure abundance values for each organism to model specific taxon compositions
* provides a population sampler to generate evolved sequences based on source genomes and a given evolutionary tree
* can be controlled via graphical user interface or in command line mode

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