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Table 4 Performance profile of Parsnp runtime (MUM + alignment) on all evaluated datasets

From: The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

Dataset Num Genomes a Aligned b(Mbp) MUM c(min) MUSCLE d(min) Total e(min) Mem f(GB)
E. coli (avg) 32 142 2 2 4 2
M. tuberculosis 171 424 12 20 32 14
P. difficile 826 1,392 46 39 85 71
S. aureus SIM 10,000 21,000 668 201 869 309
  1. Results were generated on a 32-core, 2.2 GHz, 1 TB RAM Linux server. Dataset: the genome set.
  2. aThe number of genomes aligned.
  3. bTotal Mbp aligned.
  4. cThe time spent finding maximal unique matches.
  5. dThe time spent performing gapped multi-alignment with MUSCLE.
  6. eTotal Parsnp runtime (sum of MUM and MUSCLE).
  7. fMaximum memory usage.