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Short description:
Please summarise the application in a few sentences. Avoid links here. The software can be used to generate collections of synthetic reads.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Metagenomics, Genomics
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Modelling and simulation, Sequence assembly, Mapping
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
454, Illumina, Sanger,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
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.
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