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

BMC Genomics

Table 6 Comparison of seq-seq-pan and PanCake

	seq-seq-pan	PanCake	Nucmer
Time for construction (hh:mm:ss)	02:06:00	88:10:00	03:04:00
Maximum memory usage	1.20 GB	2.34 GB	0.10 GB
Pan-genome file size	198 MB	36 MB	-
Time to add genome	00:04:01	05:33:52	00:08:48
Mean time for extraction of sequence*	00:00:09	00:01:08	-
Mean time for removing genome**	00:00:19	Not available	-
Time for consensus genome creation	00:00:47	Not available	-

First we compare the run-time and memory usage of pan-genome creation for the set of 43 M. tuberculosis genomes. PanCake requires pairwise genome comparisons by nucmer. Run-time and memory requirements for nucmer are listed separately as these can be run in parallel. We also evaluate the file size of the resulting pan-genome. We clock all available features (adding a genome, extracting part of a genome or the whole genome, remove a genome and constructing a consensus genome). * Extraction times for whole genomes and parts of sequences are equal. We extracted the interval 500-1000 for all genomes. ** Each of the 43 genomes was removed from the whole set

ISSN: 1471-2164