Database creation
Last updated
Last updated
3) Download and extract , which will be fed to pATLAS.
5) Install its
7) run - the output will include a filtered. fasta file (master_fasta_*.fas
).
8) run , with CARD, ResFinder, PlasmidFinder, VFDB databases.
9) Download the necessary for the abricate2db.py script (aro_index.csv).
10) Update the git submodules (git submodule update --init --recursive
) and run - using all the previous tsv as input.
11) .
This steps are fully automated in the nextflow pipeline .
If you require to add your own plasmids to pATLAS database without asking to add them to , you can provide custom fasta files when building the database using the -i
option of . Then follow the steps .