Table 4.
Average execution times for the different bioinformatics assays and detection methods
|
Workflow step |
Database |
Detection method |
Average duration (s) |
|---|---|---|---|
|
Read trimming |
– |
– |
31.76 |
|
Assembly |
– |
– |
847.19 |
|
Contamination check |
– |
– |
77.21 |
|
Gene detection |
ResFinder |
blast |
5.35 |
|
KMA |
5.03 |
||
|
SRST2 |
27.19 |
||
|
Virulence genes |
blast |
5.30 |
|
|
KMA |
5.14 |
||
|
SRST |
36.88 |
||
|
PlasmidFinder |
blast |
5.30 |
|
|
KMA |
5.06 |
||
|
SRST2 |
24.68 |
||
|
PointFinder |
PointFinder |
– |
15.44 |
|
Serotype determination |
SeroTypeFinder |
blast |
10.72 |
|
KMA |
10.09 |
||
|
SRST2 |
55.63 |
||
|
Sequence typing |
cgMLST* |
blast |
1128.84 |
|
KMA |
3798.15 |
||
|
SRST2 |
1 006 639.45 |
Averages were calculated over ten samples analysed in triplicate for each assay, and listed values correspond to the duration of a single analysis for a single sample.
*Sequence typing results are based on extrapolation of execution time for the first 50 loci of the cgMLST scheme (out of 2513).