Three additional databases for replicon typing and plasmid typing have been integrated into
DFAST's PlasmidFinder reference data. In addition to the standard PlasmidFinder database
(enterobacteriales, Inc18, Rep1–3, RepA_N, etc.), the following are automatically fetched and registered by
dfast_file_downloader.py --plasmidfinder and used for plasmid (replicon type) typing during an
--amr run.
| DB name | Description | File | Sequences | Size | Source (figshare) |
|---|---|---|---|---|---|
| PseudomonasRepDB | Pseudomonas replicon typing database v1.0 | PseudomonasRepDB_v1.fsa | 404 | 421 KB | PseudomonasRepDB database v1.0 |
| WHRepDB | WHRepDB database v1.0 | WHRepDB_v1.fsa | 12,923 | 12 MB | WHRepDB database v1.0 |
| Acinetobacter | AcinetobacterPlasmidTyping database v3 | AcinetobacterPlasmidTyping_v3.fsa | 555 | 561 KB | AcinetobacterPlasmidTyping database v3.0 |
All are distributed in PlasmidFinder v3 format (underscore-delimited, containing no spaces) and can be used directly as blastn subjects. No prior indexing (makeblastdb / KMA) is required.
| DB name | Example header | Notes |
|---|---|---|
| PseudomonasRepDB | >PInc-1alpha__CP002151.1 | — |
| WHRepDB | >WH-A1__NZCP038616.1 | — |
| Acinetobacter | >R3-T1_1__NC010605.1 | The original headers contain spaces, so they are automatically corrected on download (spaces → underscores) |
Substitute <DB_ROOT> with your DFAST database directory (e.g. dfast_core/db).
Cloning of the standard PlasmidFinder DB and fetching/registration of the 3 additional DBs from figshare are performed automatically.
$ dfast_file_downloader.py --plasmidfinder -d <DB_ROOT>
The data is downloaded to <DB_ROOT>/plasmidfinder_db, and rows for the additional DBs are appended to
<DB_ROOT>/plasmidfinder_db/config.
plasmidfinder_db directory every time,
so the additional DBs are never registered more than once no matter how often it is run.
Plasmid (replicon type) typing is enabled with the --amr option (which includes PlasmidFinder). The additional DBs are used automatically.
$ dfast --genome your_genome.fna --amr -o OUTPUT_DIR
Matched replicon types are written to the contig (source feature) annotation and to amr_summary.tsv.
The 3 fetched additional DBs are each registered in <DB_ROOT>/plasmidfinder_db/config and used for typing.
plasmidfinder_extra_databases in the source scripts/dfast_file_downloader.py.
Direct downloads use URLs of the form ndownloader.figshare.com/files/<id>
(the figshare.com/... form of the dataset page returns an empty response and cannot be used).