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Table 1 Recall, precision and F1 score of GenAPI, panX, BPGA, Roary, PanDelos, EDGAR and SaturnV using simulated and real datasets

From: GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences

   GenAPI panX BPGA Roary PanDelos EDGAR SaturnV
S. typhia Precision 1 1 0.93 1 NA 1 1
Recall 1 1 1 1 NA 1 1
F1 1 1 0.97 1 NA 1 1
P. aeruginosab Precision 0.91 0.38 0.39 0.35 0.43 0.18 0.18
Recall 1 1 0.94 1 1 1 1
F1 0.95 0.55 0.55 0.52 0.60 0.31 0.31
E. colic Precision 0.95 0.47 0.26 0.23 0.24 0.12 0.09
Recall 0.98 1 0.88 1 0.71 1 1
F1 0.97 0.64 0.40 0.38 0.36 0.21 0.17
  1. a simulated S. typhi dataset with complete genome sequences used in Roary publication [4]; b simulated P. aeruginosa dataset with partly assembled gene instances; c real E. coli dataset [19]