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

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

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

Results were generated on a 32-core, 2.2 GHz, 1 TB RAM Linux server. Dataset: the genome set.
^aThe number of genomes aligned.
^bTotal Mbp aligned.
^cThe time spent finding maximal unique matches.
^dThe time spent performing gapped multi-alignment with MUSCLE.
^eTotal Parsnp runtime (sum of MUM and MUSCLE).
^fMaximum memory usage.

ISSN: 1474-760X