Table 2.
Performance measures of KMA, SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, for predicting genes directly from raw reads. Thresholds for predicting a gene has been set to: 90% coverage, 90% identity and a minimum depth of 5. A minimum mapping quality of 10 was used for methods relying on post processing with SAMtools and BEDTools, as this gave the best performance across the tested thresholds
| Mapping method | Post- processing method | Avg. mapping CPU time | Avg. post- processing CPU time | Peak memory | MCC |
|---|---|---|---|---|---|
| Predicting antimicrobial resistance | |||||
| KMA | NA | 00:00:24.6 | NA | 42.3 MB | 1.000 |
| SRST2 | NA | 00:10:21.3 | NA | 165.0 MB | 1.000 |
| MGmappera | NA | 00:13:14.2 | NA | 101.4 MB | 0.288 |
| BWA-MEM | SAMtools / BEDTools | 00:07:35.5 | 00:00:06.1 | 113.0 MB | 0.000 |
| BWA-MEMb | Salmon | 00:07:34.5 | 00:00:12.2 | 694.9 MB | 0.828 |
| Bowtie2 | SAMtools / BEDTools | 00:02:35.5 | 00:00:06.7 | 33.7 MB | 0.000 |
| Bowtie2b | Salmon | 00:03:16.4 | 00:02:24.5 | 935.8 MB | 0.623 |
| Minimap2 | SAMtools / BEDTools | 00:02:18.6 | 00:00:06.0 | 517.3 MB | 0.000 |
| Mapping towards cgMLST alleles | |||||
| KMA | NA | 00:07:02.1 | NA | 8.3 GB | 0.998 |
| SRST2 | NA | > 99:99:99.9 | NA | NA | NA |
| MGmappera | NA | 01:23:21.5 | NA | 8.7 GB | 0.062 |
| BWA-MEM | SAMtools / BEDTools | 02:14:50.8 | 00:14:06.7 | 8.9 GB | 0.021 |
| BWA-MEMb | Salmon | 03:22:45.4 | 04:41:09.6 | 104.2 GBP | 0.530 |
| Bowtie2 | SAMtools / BEDTools | 01:50:56.8 | 00:15:23.5 | 4.1 GB | 0.035 |
| Bowtie2b | Salmon | > 99:99:99.9 | NA | NA | NA |
| Minimap2 | SAMtools / BEDTools | 01:20:56.2 | 00:13:11.7 | 33.6 GB | 0.035 |
a MGmapper was executed on the forward reads only, as paired end mode crashed
b Report all alignments
P The post processing method was responsible for the peak memory consumption