Table 2.
WGS analysis methods evaluated in this study.
| WGS analysis method | Type of input data | Reference-based method | Adjusted for recombination or not (method used) | Whole genome alignment length before recombination correction (bps) | Number of nucleotide positions available for phylogenetic reconstruction after recombination correction (bps) |
|---|---|---|---|---|---|
| kSNP (k-mer–based) | Contigs | Reference free | No | ||
| Roary | Gene annotations (from contigs) | Reference free | Yes (ClonalFrameML) | NmB – 1117836; NmC–1347579 | NmB – 237583; NmC–496020 |
| Parsnp | Contigs | Reference-based | Yes (ClonalFrameML) | NmB – 1331883; NmC–1547169 | NmB −265861; NmC–503939 |
| SNIPPY.(hq SNP-based) | Raw reads | Reference-based | Yes (ClonalFrameML) | NmB – 2283986; NmC–2200611 | NmB – 605744; NmC–827012 |
| cgMLST | Contigs | Reference-based (core genome MLST genes) | No | ||
| MASH (k-mer–based) | Raw reads | Reference free | No | ||
| BEAST | Parsnp/SNIPPY alignment | Reference-based | Yes (ClonalFrameML) | NmB (CC32 isolates; n = 24) – 2127589; NmC (CC11 isolates; n = 71) – 1764302 | NmB – 1709526; NmC –1168741 |