ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
Fig 2
Selection of interactive GUI widgets embedded in generated HTML5 reports.
(A) Circular genome plot for a Listeria monocytogenes pseudogenome. The zoomable and scalable SVG based circular genome plot provides comprehensive information on genome features on mouseover events. Reference-guided rearranged contigs are linked to pseudogenomes for the sake of better readability. From the outermost inward: genes on the forward and reverse strand, respectively, GC content and GC skew. (B) Donut chart of MLST sequence type (ST) distribution. The MLST ST distribution of all isolates analyzed within a project is shown by and interactive donut chart. Single STs can be selected or deselected. (C) Visual representation of normalized assembly key statistics. Per-isolate assembly key statistics are normalized to minimum and maximum values within a project column-wise and visualized within an interactive data table allowing for column-based sorting and filtering for the rapid comparison of isolates and detection of outliers. (D) Antibiotic resistance profile overview widget. An antibiotic resistance profile comprising 34 distinct target drug classes is computed based on CARD annotations for each isolate and transformed into an overview widget allowing a rapid resistome comparison of all analyzed isolates. Black rectangle: a mouseover triggered tooltip describing detected antibiotic target drug resistance. (E) SNP-based approximately-maximum-likelihood phylogenetic tree. An approximately-maximum-likelihood phylogenetic tree is computed based on SNPs detected via read-mapping against a reference genome and stored in standard newick file format. The resulting tree is visualized via the interactive Phylocanvas JavaScript library providing comprehensive user interaction features, e.g. collapsing, expanding and rotating subtrees and tree type selection. (F) Parallel coordinates plot providing a multi-dimensional cohort overview of per-isolate genome metrics and characteristics. A selection of seven genome key metrics and characteristics is visualized in a parallel coordinates plot providing a multi-dimensional cohort overview enabling the rapid detection of clustered isolates and outliers. Vertical bars: key metrics or characteristic as plot dimensions; coloured horizontal lines: isolates and related values providing table-synchronized highlighting upon mouseovers.