Visualization with PyGenomeViz

The function can be invoked via Tools > Comparison and Visualization of GenBank-Files (pyGenomeViz) and allows to choose up to 10 GenBank files for visualization. It uses the program pyGenomeViz to visualize sequence comparisons. It uses pyGenomeViz' command-line tool pgv-mummer together with MUMmer to align GenBank files and displays aligned regions and genes.

For users with the Long-read Data Plasmid Transmission Analysis Module, the visualization can also be started from a Plasmid Table, where it can be used to directly compare selected plasmids. If the visualization is used that way, genes and their positions are retrieved from other Task templates and highlighted in different colors: rep(s) from the Chromosome & Plasmid Overview (green), AMR genes from the NCBI AMRFinderPlus (priority genes: red, other: orange), and mobile genetic elements that contain priority AMR targets from the CGE MobileElementFinder (light blue).

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