megares_db_4_abricate
MEGARes db was obtained here:
wget https://megares.meglab.org/download/megares_v2.00.zip
unzip megares_v2.00.zip
Notes:
- The Rscript included in this directory was used to create the abricate formatted version of this db.
- There is probably a more appropriate way to format this database for abricate.
- There are some resistance genes that require SNP confirmation included in the original MEGARes database. These have been removed.
- This now only includes sequences from the BacMet database that are classified as conferring metal/biocide resistance. All drug resistance has been removed from the reduced fasta.
How to setup this database for use with abricate:
- Download and unzip the abricate_megares_reduced.fasta.gz file from this repo.
- Ceate a 'megares' directory where abricate looks for databases. Can run the
abricate --help
command to find this path. It should be listed in the DATABASES section, next to the --datadir option.
- Move the decompressed fasta into this new directory with the name
sequences
.
- Run
abricate --setupdb
.
For example, this is how I configured it on my system:
cd ~/reference/
git clone https://github.com/Jtrachsel/megares_db_4_abricate.git
cd megares_db_4_abricate
gunzip abricate_megares_reduced.fasta.gz
cd /home/julian.trachsel/miniconda3/db # wherever your abricate install looks for dbs
mkdir megares
cp ~/reference/megares_db_4_abricate/abricate_megares_reduced.fasta ./megares/sequences
abricate --setupdb