Table 2 Performance and feature comparison of Mykrobe predictor, SeqSphere and KvarQ software.

From: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

 

Mykrobe predictor (Sa)

SeqSphere (Sa)

Mykrobe predictor (Mtb)

KvarQ (Mtb)

RAM

100 Mb

8 Gb

100 Mb

30 Mb

Time/sample on laptop

1.5 min

—

2.75 min

40 min

Time/sample on server

44 s

19 min

47 s

23 min

CPU time (Mtb validation set)

—

—

1 day

30 days

CPU time (Sa validation set)

5.8 h

6.2 days

—

—

Speciation of clinical samples

Yes

No

Yes

No (MTBC only)

  1. MTBC, Mycobacterium tuberculosis complex; Mtb, Mycobacterium tuberculosis; Sa, Staphylococcus aureus.
  2. We show elapsed time for one sample on a laptop (Macbook Air with 8 GB RAM) and a server (Dell PowerEdge R820 with 32 cores, 1 Tb RAM), and then for the entire S. aureus and M. tuberculosis validation sets StB1 (n=491) and MTBCB (n=1609) respectively. We ran KvarQ on 1 thread for ease of parallelization and comparison, as recommended by the authors. However, we ran SeqSphere on 4 threads because to use one would have taken a prohibitively long time.
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