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Table 2 Single Node performance comparison of IMOS and the original Meta-aligner

From: IMOS: improved Meta-aligner and Minimap2 On Spark

Dataset Tool Map rate (%) Accuracy (%) T=0 Accuracy (%) T=10 Accuracy (%) T=100 Time (s)
Wgsim-S0 IM 99.66 94.5 94.9 94.9 40
  Meta-aligner 95.31 93.40 93.73 93.74 58
  BWA-MEM 97.81 99.81 99.99 100 20
  Minimap2 97.44 97.94 99.99 99.99 12
Wgsim-S1 IM 99.95 97.36 97.9 97.9 97
  Meta-aligner 97.79 94.76 96.27 96.29 174
  BWA-MEM 98.89 99.78 99.99 99.99 79
  Minimap2 98.67 97.86 99.99 99.99 25
Wgsim-S2 (Indel rich) IM 99.43 87.17 95.52 96.62 360
  Meta-aligner 70.74 21.58 79.6 90.65 501
  BWA-MEM 97.65 85.42 99.94 99.97 130
  Minimap2 97.99 75.76 99.16 99.98 23
Wgsim-S3 (Mismatch rich) IM 99.46 95.13 96.62 96.62 352
  Meta-aligner 99.05 67.09 96.21 96.23 202
  BWA-MEM 98.38 82.18 90.86 99.91 134
  Minimap2 97.79 76.60 98.94 99.99 24
Wgsim-L0 (Indel rich) IM 99.96 78.04 97.27 97.37 780
  Meta-aligner 79.96 7.41 39.2 92.37 1928
  BWA-MEM 98.84 74.78 99.69 99.98 180
  Minimap2 99.04 59.02 94.58 99.98 47
Wgsim-L1 IM 99.81 99.02 99.05 99.05 438
  Meta-aligner 99.49 90.71 97.71 97.73 2306
  BWA-MEM 99.20 99.10 100 100 118
  Minimap2 99.05 98.06 100 100 33
Wgsim-L2 (Indel rich) IM 98.63 76.61 99.14 99.14 1954
  Meta-aligner 95.97 5.02 31.56 94.23 6103
  BWA-MEM 99.22 75.00 99.77 99.98 318
  Minimap2 99.22 58.69 94.74 99.98 72
SimLoRD IM 92.79 89.75 93.69 93.69 991
  Meta-aligner 92.79 0.08 22.15 42.09 1851
  BWA-MEM 92.43 85.46 95.98 97.65 458
  Minimap2 92.43 79.88 98.07 99.89 75
PBSim IM 99.75 88.60 95.81 95.96 1098
  Meta-aligner 90.55 1.05 5.15 40.49 3918
  BWA-MEM 98.65 65.22 96.01 97.65 567
  Minimap2 98.93 54.50 95.56 99.98 78
SRX533609 IM 92.35 - - - 9031
  Meta-aligner 70.05 - - - 24,393
  BWA-MEM 92.75 - - - 3653
  Minimap2 89.58 - - - 348
ERX1366175 IM 97.33 - - - 2780
  Meta-aligner 88.15 - - - 14,303
  BWA-MEM 95.24 - - - 1512
  Minimap2 94.14 - - - 146