Mash Genotyping Library

Mash typing settings can be modified in the Genotyping Libraries tab of the Task Template editor.

Plasmids can be filtered for AMR targets. This requires that a Sample also has a "NCBI AMRFinderPlus" Task Entry. Otherwise no typing can be done, except for the "All plasmids" option.

The following filtering options are available:

• Priority AMR targets carrying plasmids
  Plasmids that carry priority AMR targets
• Non-priority AMR target only carrying plasmids
  Plasmids that carry non-priority AMR targets but no priority AMR targets
• AMR targets carrying plasmids
  Plasmids that carry non-priority AMR targets or priority AMR targets
• All plasmids except priority AMR targets carrying ones
  Plasmids that carry no AMR targets or non-priority AMR targets
• All plasmids. This option does not require a "NCBI AMRFinderPlus" Task Entry.
• Carbapeneme AMR targets carrying plasmids
  Plasmids that carry Carbapeneme AMR targets
• All plasmids except Carbapeneme AMR targets carrying ones
  Plasmids that carry no Carbapeneme AMR targets

Plasmid Typing can be skipped for Samples with more than 30 contigs (e.g., for short-read data).

The max. MASH distance thresholds up to which plasmids are listed can be entered. Default thresholds are:

• with "ignore > 30 contigs": default threshold is 0.001
• without "ignore > 30 contigs": default threshold is 0.025

For long-read data, the distance can be adjusted for plasmids with different sizes. The max allowed size difference and the distance correction per 1% size difference can be entered. If the size difference is greater than the max allowed value, no distance correction is used. Default values are:

• 0.0003 Mash dist per 1% size difference
• Max. allowed size difference of 40%

If a new plasmid Typing is created, the Mash sketch size can be specified. A sketch size of 1000 is the default setting. The k-mer size is fixed at 21 and cannot be changed.

The button View DB content opens a Mash database view window.