Table 3 cgMLST precision (i.e mean percentage ± standard deviation) of the workflows BIGSdb (n = 420), INNUENDO (n = 336), GENPAT (n = 420), SeqSphere (n = 420), BioNumerics (n = 420) and MentaLiST (n = 420) according to targeted read (Dr) and kmer (Dk) depth (X) from BBNorm downsampling (read length R = 150 and kmer size K = 30) of Listeria monocytogenes paired-end reads from reference genomes ATCC19114, ATCC19115 and ATCCBAA679. The cgMLST schema harbors 1748 loci. NA means not applicable: Because of internal firewall, the INNUca assembler integrated into the cgMLST workflow INNUENDO cannot not perform assemblies of paired-end reads with read depth of coverage of 20X (n = 42) and 10X (n = 42)
From: In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes
Reference | Targeted depth of coverage | BIGSdb | INNUENDO | GENPAT | SeqSphere | BioNumerics | MentaLiST |
|---|---|---|---|---|---|---|---|
ATCC19114 | Dr100-Dk75 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.79 ± 0.04 | 99.71 ± 0.02 |
Dr90-Dk68 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.80 ± 0.03 | 99.71 ± 0.02 | |
Dr80-Dk60 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.80 ± 0.04 | 99.71 ± 0.02 | |
Dr70-Dk53 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.80 ± 0.03 | 99.71 ± 0.02 | |
Dr60-Dk45 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.80 ± 0.04 | 99.71 ± 0.02 | |
Dr50-Dk38 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.79 ± 0.06 | 99.70 ± 0.02 | |
Dr40-Dk31 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.78 ± 0.06 | 99.54 ± 0.12 | |
Dr30-Dk23 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 99.71 ± 0.02 | 97.69 ± 0.10 | 93.77 ± 0.82 | |
Dr20-Dk16 | 99.71 ± 0.02 | NA | 99.71 ± 0.02 | 99.71 ± 0.02 | 96.87 ± 0.22 | 36.67 ± 1.70 | |
Dr10-Dk8 | 99.44 ± 0.13 | NA | 99.51 ± 0.02 | 99.51 ± 0.09 | 69.63 ± 2.34 | 0.07 ± 0.07 | |
ATCC19115 | Dr100-Dk75 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 99.99 ± 0.02 | 100 ± 0.00 |
Dr90-Dk68 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 99.99 ± 0.03 | 100 ± 0.00 | |
Dr80-Dk60 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 99.99 ± 0.03 | 100 ± 0.00 | |
Dr70-Dk53 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 100 ± 0.02 | 100 ± 0.00 | |
Dr60-Dk45 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 100 ± 0.00 | 100 ± 0.02 | |
Dr50-Dk38 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 99.99 ± 0.02 | 100 ± 0.02 | |
Dr40-Dk31 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 99.99 ± 0.03 | 99.85 ± 0.11 | |
Dr30-Dk23 | 100 ± 0.00 | 99.83 ± 0.00 | 99.83 ± 0.00 | 100 ± 0.00 | 99.91 ± 0.09 | 93.76 ± 0.84 | |
Dr20-Dk16 | 100 ± 0.00 | NA | 99.83 ± 0.00 | 100 ± 0.00 | 99.15 ± 0.26 | 37.04 ± 2.01 | |
Dr10-Dk8 | 99.77 ± 0.14 | NA | 99.64 ± 0.11 | 99.78 ± 0.13 | 72.41 ± 1.40 | 0.09 ± 0.05 | |
ATCCBAA679 | Dr100-Dk75 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 100 ± 0.02 | 99.98 ± 0.04 | 99.96 ± 0.03 |
Dr90-Dk68 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 100 ± 0.02 | 99.99 ± 0.02 | 99.95 ± 0.03 | |
Dr80-Dk60 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 100 ± 0.02 | 99.98 ± 0.04 | 99.95 ± 0.02 | |
Dr70-Dk53 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 100 ± 0.02 | 99.97 ± 0.04 | 99.94 ± 0.03 | |
Dr60-Dk45 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 99.99 ± 0.02 | 99.97 ± 0.03 | 99.95 ± 0.03 | |
Dr50-Dk38 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 100 ± 0.02 | 99.97 ± 0.04 | 99.94 ± 0.04 | |
Dr40-Dk31 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 100 ± 0.02 | 99.98 ± 0.04 | 99.81 ± 0.08 | |
Dr30-Dk23 | 100 ± 0.02 | 99.82 ± 0.02 | 99.82 ± 0.02 | 100 ± 0.02 | 99.92 ± 0.05 | 94.19 ± 1.02 | |
Dr20-Dk16 | 100 ± 0.02 | NA | 99.82 ± 0.02 | 100 ± 0.02 | 99.09 ± 0.25 | 37.18 ± 1.77 | |
Dr10-Dk8 | 99.69 ± 0.14 | NA | 99.56 ± 0.10 | 99.75 ± 0.10 | 72.49 ± 2.33 | 0.13 ± 0.06 |