seq-seq-pan: building a computational pan-genome data structure on whole genome alignment

BMC Genomics

Table 5 Run-time and memory usage. We compare seq-seq-pan to other whole genome aligners in terms of run-time and memory usage. Time and memory are indicated for single-threaded processes. Individual steps for TBA can be run in parallel

	Elapsed wall clock time (hh:mm)	Maximum resident set size (GB)
Simulated dataset (13 genomes)
seq-seq-pan	00:30	0.77
progressiveMauve	02:33	4.93
Mugsy	01:08	1.01
progressiveCactus	03:41	1.00
TBA	04:59	0.34
M. tuberculosis dataset (43 genomes)
seq-seq-pan	02:06	1.20
progressiveMauve	09:03	2.79
Mugsy*	14:52	3.26
progressiveCactus	47:09	5.54
TBA	386 days	1.32
S. aureus dataset (144 genomes)
seq-seq-pan	08:55	4.27
E. coli dataset (207 genomes)
seq-seq-pan	68:19	8.5

For the larger datasets (S.aureus and E.coli) only seq-seq-pan was used for the alignment due to run-time limitation of other tools. * Aligning 43 M. tuberculosis genomes caused a segmentation fault in Mugsy. This table lists data for aligning 39 genomes with Mugsy, but the whole set of 43 genomes for all other tools

ISSN: 1471-2164