TABLE 6

Overview of complete analysis software suitesa

Software suiteConceptRAM compatibility (Gb)Run time (h)No. of schemesPrice ($)Source or Web addressInput formatOutput format(s)
Commercial
    BioNumerics 7.6.2Suite containing multiple modules, thereby having many functionalities; able to perform wgMLSTNDND14Request quotebApplied MathsFASTQDepends 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 definitions16–32cND72,500dRidom BioinformaticsFASTQCT, 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 inferenceNANA19eFreehttps://www.ncbi.nlm.nih.gov/pathogens/FASTQWeb-accessible SNP tree, AMR data
  • a ND, no data; NA, not applicable.

  • b Cost needs to be requested and is dependent on the number of modules.

  • c According to the manufacturer.

  • d One-year, 2-user accounts (academic/governmental).

  • e Numbers of species and groups of species, as no schemes apply.