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Short description:
Please summarise the application in a few sentences. Avoid links here. Nesoni is a high-throughput sequencing data analysis toolset.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
RNA-Seq alignment, SNP detection, Phylogenetics,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Sequence alignment,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina, 454, ABI SOLiD,
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):
Victorian Bioinformatics Consortium
Nesoni is a high-throughput sequencing data analysis tool set, which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced. Our work is largely with bacterial genomes, and the design trade-offs in nesoni reflect this. Nesoni focusses on analysing the alignment of reads to a reference genome. We use the [[SHRiMP]] read aligner, as it is able to detect small insertions and deletions in addition to SNPs. Nesoni can call a consensus of read alignments, taking care to indicate ambiguity. This can then be used in various ways: to determine the protein level changes resulting from SNPs and indels, to find differences between multiple strains, or to produce n-way comparison data suitable for phylogenetic analysis in [[SplitsTree4]]. Alternatively, the raw counts of bases at each position in the reference seen in two different sequenced strains can compared using Fisher's Exact Test.
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