The choice here is offered between virtually setup-free pay-per-use cloud solutions (e.g. In BIONUMERICS, demanding calculations such as de novo assemblies can be performed on an external calculation engine. based on a de novo assembly, followed by a BLAST search.This plugin provides a fully automated pipeline for identifying alleles based on whole genome sequence data.īIONUMERICS uses two methods to identify alleles: Whereas only a limited number of people will have access to the curated organism-specific reference database, most users will only need the WGS tools plugin. Creation of sub-schemes such as MLST, eMLST, rMLST starting from wgMLST.The wgMLST curator plugin offers a full range of automated curation tools needed to set up and maintain a wgMLST schema for any organism of choice. BIONUMERICS for whole genome multi locus sequence typing The wgMLST curator and WGS tools plugins To accommodate for this, automated curation tools are provided. In absence of suitable automated tools, it would be a daunting task to maintain a consistent allele assignment for thousands of loci. The major drawback of the technique is that it requires allele curation. This approach might be biologically more relevant than approaches that consider only point mutations. In contrast to whole genome SNP analysis, wgMLST is based on the concept of allelic variation, meaning that recombinations and deletions or insertions of multiple positions are counted as single evolutionary events. Since many more loci (typically 1500 – 4000) are considered in wgMLST, a much higher typing resolution can be obtained. Unique sequences for each locus are assigned allele numbers and bacterial strains are identified based on their allelic profiles, which is the combination of the seven allele numbers.Īs next-generation sequencing, which offers a fast and cost-effective way to sequence bacterial genomes, is increasingly replacing Sanger sequencing, conventional MLST can be extended to whole genome MLST (wgMLST). Classical MLST schemes typically define seven loci (housekeeping genes), which are sequenced using Sanger technology. Multi-locus sequence typing ( MLST) has proven its usefulness for molecular typing of bacteria over the last 15 years.
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