Table 3.
Build times, memory consumption and index sizes at taxonomic level
| Reference | Method | Time | Memory | Index size |
|---|---|---|---|---|
| RefSeq-OLD | Centrifuge | 02:51:03 | 98 | 4 |
| Clark | 04:07:56 | 150 | 32 | |
| Diamond | 00:08:07 | 28 | 3 | |
| Ganon | 00:02:08 | 22 | 15 | |
| Kraken | 02:04:16 | 87 | 73 | |
| Kraken2 | 00:17:28 | 13 | 10 | |
| RefSeq-CG-top-3 | Centrifuge | 06:51:25 | 262 | 12 |
| Clark | 08:45:31 | 243 | 81 | |
| Diamond | 00:10:33 | 27 | 9 | |
| Ganon | 00:07:01 | 68 | 62 | |
| Kraken | 04:53:31 | 195 | 184 | |
| Kraken2 | 00:45:25 | 29 | 26 | |
| RefSeq-ALL-top-3 | Diamond | 00:36:23 | 30 | 70 |
| Ganon | 00:54:48 | 248 | 249 | |
| Kraken2 | 05:04:24 | 124 | 123 |
Note: Memory and index size in GiB. All tools build at taxonomic leaf nodes (taxid) besides clark building at species level. Tools running more than 24 h to build were not considered. A total of 48 threads were used for all tools. Computer specifications and parameters used are in the Supplementary Sections S2.1 and S2.4. Krakenuniq was not evaluated on taxonomic level since it runs exactly the same base algorithm as kraken in this configuration.