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Table 2 Species-level classification accuracy and speed of CLARK, KRAKEN , and NBC for four simulated metagenomes

From: CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

  HiSeq MiSeq simBA-5 simHC.20.500
  Prec Sens Speed Prec Sens Speed Prec Sens Speed Prec Sens Speed
NBC (k=15) 68.67 68.70 0.008 68.33 68.33 0.007 91.74 91.74 0.007 94.32 94.32 0.005
Clark (k=20) 69.44 61.46 272 70.72 62.45 239 91.32 82.48 269 94.34 94.32 96
Kraken (k=31) 74.00 53.49 2,332 77.72 58.72 1,361 92.99 78.70 1,976 84.67 84.31 237
Clark (k=31) 86.74 58.59 3,011 89.49 61.84 1,566 98.85 76.80 2,855 94.67 94.26 251
Kraken-Q (k=31) 75.88 50.78 6,224 78.07 53.68 5,308 92.67 74.39 7,023 82.40 74.84 3,809
Clark-E (k=31) 90.08 55.18 30,976 94.31 58.36 24,029 98.92 66.02 24,996 92.78 92.38 15,583
Clark-l (k=27) 85.35 53.95 1,676 85.89 64.91 904 85.55 46.28 1,702 94.06 93.53 141
  1. Precision and sensitivity are expressed as percentages, while speed is expressed in 103 reads per minute for NBC, KRAKEN, and CLARK on the classification of “HiSeq”, “MiSeq”, “simBA-5” and “simHC.20.500” metagenome datasets against the 1473 species-level targets, in single-threaded mode.