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Pre‐trained data
To improve the efficiency of the algorithm, we first preprocess the reference genome database by reducing its size based on certain parameters, namely, K-mer size and ANI threshold. The user choose their own reference genome database and customize these parameter values to suit their research needs. Here, we provide some pre-trained databases generated using some of the popular databases and commonly used parameters.
The exact algorithm for this process can be found in Algorithm 4 of the preprint. In short, given a collection of reference genomes, we first sketch them based on the K-mer size given. If two genome sketches have an ANI above the threshold given, the two genomes will be regarded as identical. The smaller of the two will then be removed and the larger one will be used as the representative of the two.
These databases were pre-trained using the 214 release of bacterial and archaeal data from GTDB, which GTDB spans 402,709 genomes organized into 85,205 species clusters. For more information on the raw data, refer to the statistics here.
| K-mer size | ANI | Zip file |
|---|---|---|
| 21 | 0.8 | Download |
| 21 | 0.95 | Download |
| 21 | 0.995 | Download |
| 21 | 0.9995 | Download |
| 31 | 0.8 | Download |
| 31 | 0.95 | Download |
| 31 | 0.995 | Download |
| 31 | 0.9995 | Download |
| 51 | 0.8 | Download |
| 51 | 0.95 | Download |
| 51 | 0.995 | Download |
| 51 | 0.9995 | Download |
| K-mer size | ANI | Zip file |
|---|---|---|
| 21 | 0.8 | Download |
| 21 | 0.95 | Download |
| 21 | 0.995 | Download |
| 21 | 0.9995 | Download |
| 31 | 0.8 | Download |
| 31 | 0.95 | Download |
| 31 | 0.995 | Download |
| 31 | 0.9995 | Download |
| 51 | 0.8 | Download |
| 51 | 0.95 | Download |
| 51 | 0.995 | Download |
| 51 | 0.9995 | Download |
| K-mer size | ANI | Zip file |
|---|---|---|
| 21 | 0.8 | Download |
| 21 | 0.95 | Download |
| 21 | 0.995 | Download |
| 21 | 0.9995 | Download |
| 31 | 0.8 | Download |
| 31 | 0.95 | Download |
| 31 | 0.995 | Download |
| 31 | 0.9995 | Download |
| 51 | 0.8 | Download |
| 51 | 0.95 | Download |
| 51 | 0.995 | Download |
| 51 | 0.9995 | Download |
| K-mer size | ANI | Zip file |
|---|---|---|
| 21 | 0.8 | Download |
| 21 | 0.95 | Download |
| 21 | 0.995 | Download |
| 21 | 0.9995 | Download |
| 31 | 0.8 | Download |
| 31 | 0.95 | Download |
| 31 | 0.995 | Download |
| 31 | 0.9995 | Download |
| 51 | 0.8 | Download |
| 51 | 0.95 | Download |
| 51 | 0.995 | Download |
| 51 | 0.9995 | Download |