Table 1 Performance of KMA, SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, on simulated data generated from the ResFinder database. A minimum mapping quality of 1 was used to ensure reproducibility
From: Rapid and precise alignment of raw reads against redundant databases with KMA
Method / Performance | Single end read set | Paired end read set | ||||
|---|---|---|---|---|---|---|
MCC | Sensitivity | PPV | MCC | Sensitivity | PPV | |
KMA | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
SRST2 | 0.591 | 0.999 | 0.350 | 0.659 | 0.999 | 0.436 |
MGmapper | 0.676 | 0.457 | 1.000 | 0.443 | 0.196 | 1.000 |
BWA-MEM | 0.585 | 0.342 | 1.000 | 0.580 | 0.337 | 1.000 |
Bowtie2 | 0.480 | 0.480 | 0.480 | 0.577 | 0.577 | 0.577 |
Minimap2 | 0.591 | 0.353 | 0.988 | 0.671 | 0.455 | 0.991 |
BWA-MEM / Salmon | 0.720 | 0.720 | 0.720 | 0.500 | 0.353 | 0.707 |
Bowtie2 / Salmon | 0.390 | 0.389 | 0.398 | 0.250 | 0.177 | 0.368 |