TABLE 6.

Overview of complete analysis software suites^a

Software suite	Concept	RAM compatibility (Gb)	Run time (h)	No. of schemes	Price ($)	Source or Web address	Input format	Output format(s)
Commercial
BioNumerics 7.6.2	Suite containing multiple modules, thereby having many functionalities; able to perform wgMLST	ND	ND	14	Request quoteb	Applied Maths	FASTQ	Depends on module
Ridom SeqSphere+	Suite dedicated to outbreak analyses; customizable automation flows for processing raw reads to phylogeny using either cgMLST or wgMLST; for cgMLST, it includes CT definitions	16–32c	ND	7	2,500d	Ridom Bioinformatics	FASTQ	CT, phylogeny
Free
NCBI Pathogen Detection (beta)	NCBI-provided Web service with main focus on detection of foodborne pathogens; automated flow from raw sequences to phylogeny inference	NA	NA	19e	Free	https://www.ncbi.nlm.nih.gov/pathogens/	FASTQ	Web-accessible SNP tree, AMR data

^aND, no data; NA, not applicable.

^bCost needs to be requested and is dependent on the number of modules.

^cAccording to the manufacturer.

^dOne-year, 2-user accounts (academic/governmental).

^eNumbers of species and groups of species, as no schemes apply.