Table 2 Runtimes of deltaRpkm pipeline, versus two most similar tools. Since deltaRpkm does not require any assembly and annotation steps, it is difficult to compare it with other methods
Method | Small dataset | Large dataset |
|---|---|---|
deltaRpkm | N = 31, runtime = ~ 40 s (L.monocytogenes, ~ 3 Mb) | N = 225, runtime = ~ 20 min (L.monocytogenes) |
Roary [6] | N = 24, runtime = ~ 6 min (S.enterica, ~ 4.8 Mb) [6] | N = 1000, runtime = ~ 250 min (S.enterica serovar Typhi) [6] |
BPGA [7] | N = 28, runtime = ~ 3 min (S.pyogenes, ~ 1.8 Mb) [7] | N = 1000, runtime = ~ 420 min (S.pyogenes) [7] |