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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
  1. MCC Matthews correlation coefficient, PPV Positive Prediction Value