This release adds a Sunburst visualisation to the LINvis tool and a plugin wrapper for the FlavoTyper tool used to serotype Flavobacterium psychrophilum.
LINvis Sunburst visualisation
LINvis previously only provided a circle-packing visualisation. It is important to note that in circle-packing nodes are constrained by the packing of descendents, so outer nodes may have inconsistent sizes even when their leaf totals are the same. The size of outer nodes is more dependent on the number of unique inner nodes and how they branch. With Sunburst visualisations, all nodes are consistently sized relative to their frequency.
Selecting the sunburst visualisation displays a series of concentric circles with each ring representing a different LIN threshold with each prefix value at that threshold sized proportionally to its frequency. Segments are coloured by the top-level threshold. Controls are similar to those for the circle packing, with the only difference being the automatic labelling using a count of labels with annotations showing the largest segments.
Searching for isolates works in exactly the same way as for circle packing, with each containing segment highlighted.
Clicking any segment will redraw the hierarchy centred on that position, e.g. clicking on the segment arrowed…
… shows the hierarchy where all records have the same top-level threshold value.
FlavoTyper
FlavoTyper is a bioinformatics tool that performs in silico serotyping of Flavobacterium psychrophilum genome assemblies. Phenotypic characterization of this pathogen (including serotyping based on the structural variations in the O-polysaccharide moiety of cell surface lipopolysaccharide) provides critical information for epidemiological surveillance, outbreak investigation, and the design of effective vaccines. FlavoTyper enables this characterization directly from genome assemblies, making serotyping scalable, reproducible, and independent of wet-lab assays.
FlavoTyper was developed by Salma Mbarki in the Laboratory of Eric Duchaud, Unité Virologie et Immunologie Moléculaires (INRAE), France. The code can be found at https://pypi.org/project/flavotyper/.
The tool is only enabled on the PubMLST Flavobacterium psychrophilum database.
Results from running FlavoTyper will be stored in the database and once run are available for display within an isolate record.
Full Changelog: v_1.53.3...v_1.53.4