Difference between revisions of "MetaSim"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary= | + | |sw summary=The software can be used to generate collections of synthetic reads. |
| − | |||
|bio domain=Metagenomics, Genomics | |bio domain=Metagenomics, Genomics | ||
|bio method=Simulation, Assembly, Mapping | |bio method=Simulation, Assembly, Mapping | ||
| + | |bio tech=454, Illumina, Sanger, | ||
|language=Java | |language=Java | ||
| − | |licence=Free for academic use, | + | |licence=Free for academic use, |
}} | }} | ||
| + | The 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. | ||
{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Revision as of 09:39, 7 September 2011
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Application data |
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| Biological application domain(s) | Metagenomics, Genomics |
|---|---|
| Principal bioinformatics method(s) | Simulation, Assembly, Mapping |
| Technology | 454, Illumina, Sanger |
| Maintained? | Maybe |
| Programming language(s) | Java |
| Licence | Free for academic use |
Summary: The software can be used to generate collections of synthetic reads.
"Error: no local variable "counter" was set." is not a number.
The 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.
Links
References
To add a reference for MetaSim, enter the PubMed ID in the field below and click 'Add'.
Search for "MetaSim" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
