Whole genome SNP analysis

BIONUMERICS features an analysis suite that allows you to detect Single Nucleotide Polymorphisms (SNPs) on whole genomes sequences and perform cluster analyses on the resulting whole genome SNP (wgSNP) matrix.

SNP dendrogram

With an appropriately chosen reference sequence, wgSNP offers the ultimate resolution in strain typing!

Start from the raw sequence reads

Sequence assemblyThe most trivial way to ensure that genomic sequences are collinear for all isolates under investigation, is to map their raw sequence reads against the same reference sequence.

You can do this locally on your desktop computer or on the calculation engine.

Filter out relevant SNPs

In addition to true point mutations, observed differences with the reference may be due to e.g. sequencing errors or larger indels and rearrangements. For phylogenetic analyses and strain typing it is therefore very important to retain only the relevant, high-quality SNPs.

A wide range of SNP filters is available in BIONUMERICS, covering any possible scenario.

SNP filtersThe all-new SNP analysis window provides plenty of visual feedback to assess the effect of SNP filters and offers an easy link to the sequences and assemblies.

Convenient SNP templates

A SNP template is a set of SNP filters with their settings. BIONUMERICS offers default SNP templates, which cover most common use scenarios. In addition, you can create your own SNP templates, optimized for your research.

SNP distance coefficientIn routine applications, you can create a wgSNP clustering in just a few mouse clicks. A new “Categorical differences” coefficient is available for wgSNP cluster analysis.

Integration with the calculation engine

Submit jobs dialogInstall the WGS tools plugin to perform time-consuming reference mappings on the calculation engine and to combine wgSNP with wgMLST results.

Supported in BIONUMERICS configurations: