Table 2.
Adjusted thresholds for optimised clustering concordance between cgMLST methods and between cgMLST and SNP methods. Clustering by cgMLST methods at published thresholds [12, 13] (in bold type on the left) was set as reference for the adjustment of clustering thresholds for other methods. The columns show the different comparison methods and the threshold values (alleles or SNPs) at which the greatest possible agreement among the clustering with the respective reference method was achieved based on adjusted Wallace coefficients presented in Fig. 5. As cluster comparison is direction-dependent, the table must be read from the left to the right
|
cgMLST |
SNP |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
|
General reference |
MLST CC-specific reference |
||||||||||
|
Allele threshold |
Ridom_Ruppitsch |
chewBBACA_Ruppitsch |
BioNumerics_Moura |
Snippy_EGDe |
BioNumerics_EGDe |
Snippy_closed |
Snippy_draft |
BioNumerics_closed |
BioNumerics_draft |
||
|
cgMLST |
Ridom_ Ruppitsch |
7 |
6 |
6 |
9–10 |
4 |
11 |
12 |
12 |
11–12 |
|
|
chewBBACA_ Ruppitsch |
7 |
7 |
9–10 |
4 |
11 |
12 |
12 |
11–12 |
|||
|
BioNumerics_ Moura |
8 |
7 |
13 |
4 |
12 |
12 |
11 |
11–12 |
|||
|
Ridom_ Ruppitsch |
10 |
10 |
10 |
15 |
5 |
19 |
19 |
18 |
18 |
||
|
chewBBACA_ Ruppitsch |
10 |
10 |
15 |
5 |
20 |
18–19 |
18 |
18 |
|||
|
BioNumerics_ Moura |
11 |
11 |
18 |
6 |
20 |
22 |
19 |
20 |
|||