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