/megares_db_4_abricate

abricate formatted megares db

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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:

  1. The Rscript included in this directory was used to create the abricate formatted version of this db.
  2. There is probably a more appropriate way to format this database for abricate.
  3. There are some resistance genes that require SNP confirmation included in the original MEGARes database. These have been removed.
  4. 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:

  1. Download and unzip the abricate_megares_reduced.fasta.gz file from this repo.
  2. 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.
  3. Move the decompressed fasta into this new directory with the name sequences.
  4. 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