Table 5. Effect of the genome source (either RefSeq or GenBank) on clustering results using Archaea as a test case.
The runs carried out on GenBank Archaea used canonical k-mers. The JI runs used a distance threshold of 0.90 and the IGF runs a threshold of 0.80. The super-phyla are the Asgard group, the TACK group and the DPANN group. Unclassified genomes are genomes without a phylum in the NCBI Taxonomy. JI: Jaccard Index; IGF: Identical Genome Fraction.
| Source | # super-phyla | # phyla | # unclassified genomes | # genomes | Clustering mode |
|---|---|---|---|---|---|
| RefSeq | 3 | 7 | 0 | 941 | NA |
| GenBank | 3 | 24 | 265 | 4129 | NA |
| JI RefSeq | 2 | 6 | 0 | 46 | strict |
| JI RefSeq | 2 | 6 | 0 | 29 | loose |
| IGF RefSeq | 2 | 6 | 0 | 38 | strict |
| IGF RefSeq | 1 | 3 | 0 | 16 | loose |
| JI GenBank | 3 | 17 | 38 | 313 | strict |
| JI GenBank | 3 | 15 | 18 | 145 | loose |
| IGF GenBank | 2 | 10 | 6 | 34 | strict |
| IGF GenBank | 1 | 1 | 0 | 1 | loose |