Table 2.

Presets for Lyve-SET.

Name	Settings
lambda	min_coverage = 4 min_alt_frac = 0.75 mask-phages = 0
vibrio_cholerae	min_coverage = 10 min_alt_frac = 0.75
listeria_monocytogenes	min_coverage = 10 min_alt_frac = 0.75
salmonella_enterica	min_coverage = 20 min_alt_frac = 0.95 allowedFlanking = 5 mask-phages = 1
escherichia_coli	min_coverage = 20 min_alt_frac = 0.95 allowedFlanking = 5 mask-phages = 1
clostridium_botulinum	min_coverage = 10 min_alt_frac = 0.75 allowedFlanking = 5 mask-phages = 1 mask-cliffs = 1

Some settings that have been empirically determined are in a configuration file in the Lyve-SET package. These settings can be revised by individual users in the file presets.conf. For many species such as Campylobacter jejuni, we have not yet determined the most optimal preset options. However in the future these settings could be added upon or revised following any observations we may make in the due course of outbreak investigations. In each Lyve-SET run, these settings and their values are displayed in the log file, whether or not they were explicitly defined and whether or not the preset configurations were explicitly called.