# Database creation

![Workflow db creation](/files/-LJYLWJ6rt8FQSu-7MYc)

## Workflow for database creation

1\) Download plasmid sequences available in [NCBI refseq](ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/).

2\) Extract fasta from tar.gz.

3\) Download and extract [NCBI taxonomy](ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz), which will be fed to pATLAS.

4\) Clone this repository:

```
git clone https://github.com/tiagofilipe12/pATLAS
```

5\) Install its [dependencies](https://github.com/tiagofilipe12/pATLAS#dependencies)

6\) Configure the database:

```
createdb <database_name>
pATLAS/patlas/db_manager/db_create.py <database_name>
```

7\) run [MASHix.py](https://github.com/tiagofilipe12/pATLAS#mashixpy) - the output will include a filtered. fasta file (`master_fasta_*.fas`).

8\) run [ABRicate](https://github.com/tseemann/abricate), with CARD, ResFinder, PlasmidFinder, VFDB databases.

```
# e.g.
abricate --db card <master_fasta*.fas> > abr_card.tsv
abricate --db resfinder <master_fasta*.fas> > abr_resfinder.tsv
abricate --db vfdb <master_fasta*.fas> > abr_vfdb.tsv
abricate --db plasmidfinder <master_fasta*.fas> > abr_plasmidfinder.tsv
```

9\) Download the [card index](https://card.mcmaster.ca/download/0/broadstreet-v2.0.2.tar.gz) necessary for the abricate2db.py script (aro\_index.csv).

10\) Update the git submodules (`git submodule update --init --recursive`) and run [abricate2db.py](https://github.com/tiagofilipe12/pATLAS#abricate2dbpy) - using all the previous tsv as input.

```
# e.g.
abricate2db.py -i abr_plasmidfinder.tsv -db plasmidfinder \
    -id 80 -cov 90 -csv aro_index.csv -db_psql <database_name>
```

11\) [dump database to a sql file](/docs/api/database_creation.md#database-export).

### Automation of this steps

This steps are fully automated in the nextflow pipeline [pATLAS-db-creation](https://github.com/tiagofilipe12/pATLAS-db-creation).

### Creating a custom version of pATLAS

If you require to add your own plasmids to pATLAS database without asking to add them to [pATLAS website](https://github.com/tiagofilipe12/pATLAS/tree/70001e32d809856e7f793ffcebd527d812e7824e/docs/www.patlas.site), you can provide custom fasta files when building the database using the `-i` option of [MASHix.py](https://github.com/tiagofilipe12/pATLAS#mashixpy). Then follow the steps [described above](/docs/api/database_creation.md#workflow-for-database-creation).


---

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