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Table 6 Comparison of seq-seq-pan and PanCake

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

  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 -
  1. 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