Long Read Module (LRM) that includes the ONT Data Assembly and Long Read Data Plasmid Transmission Analysis sub-modules.

The ONT Data Assembly sub-module enables users to assemble Oxford Nanopore Technologies (ONT) FASTQ-files. The sub-module requires at least 32 GB RAM. It can also directly monitor and process MinKNOW run data.

The basis for this sub-module is the usage of the Chromosome and Plasmids Overview (MOB-suite), NCBI AMRFinderPlus, and CGE MobileElementFinder task templates that are available for all users. The Long Read Data Plasmid Transmission Analysis sub-module then enables users to detect plasmid transmissions using the Mash Plasmid Typing function. Plasmids can be aligned and visually compared using an integrated version of pyGenomeViz.