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ResFinder Database documentation

The ResFinder database is a curated database of acquired resistance genes.

Content of the repository

  1. <AMR class>.fsa - DNA sequence of the genes from a specified AMR class
  2. phenotypes.txt - Translation table for genotype to phenotype prediction
  3. phenotype_panels.txt - For selected species, lists the relevant phenotypes
  4. INSTALL.py - Script for indexing the database with KMA

Installation

Clone the database

git clone https://git@bitbucket.org/genomicepidemiology/resfinder_db.git

The database can be used with BLAST as-is.

If you want to use the database with the stand-alone ResFinder tool, and wishes to use the mapping based method (available from ResFinder version 4.0.0), the database needs to be indexed.

Installing KMA (optional):

If you are running the stand-alone ResFinder in docker, you may be able to skip installing KMA, and just rely on the temporary KMA installation done by the INSTALL script (or if you are just lazy and don't want to type the path to kma).

If you are not running ResFinder stand-alone in docker, you will need to install KMA, if the mapping based method is needed (recommended).

Download and install KMA

# Go to the directory in which you want KMA installed
cd /some/path
# Clone KMA
git clone https://bitbucket.org/genomicepidemiology/kma.git
# Go to kma directory and compile code
cd kma && make

Indexing with INSTALL.py

If you have KMA installed you either need to have the kma_index in your PATH or you need to provide the path to kma_index to INSTALL.py

a) Run INSTALL.py in interactive mode

# Go to the database directory
cd path/to/resfinder_db
python3 INSTALL.py

If kma_index was found in your path a lot of indexing information will be printed to your terminal, and will end with the word "done".

If kma_index wasn't found you will recieve the following output:

KMA index program, kma_index, does not exist or is not executable
Please input path to executable kma_index program or choose one of the options below:
    1. Install KMA using make, index db, then remove KMA.
    2. Exit

You can now write the path to kma_index and finish with <enter> or you can enter "1" or "2" and finish with <enter>.

If "1" is chosen, the script will attempt to install kma in your systems default temporary location. If the installation is successful it will proceed to index your database, when finished it will delete the kma installation again.

b) Run INSTALL.py in non_interactive mode

# Go to the database directory
cd path/to/resfinder_db
python3 INSTALL.py /path/to/kma_index non_interactive

The path to kma_index can be omitted if it exists in PATH or if the script should attempt to do an automatic temporary installation of KMA.

It is possible to index the databases manually, but is generally not recommended as it is more prone to error. If you choose to do so, be aware of the naming of the indexed files.

This is an example of how to index the ResFinder database files:

# Go to the database directory
cd path/to/resfinder_db
# create indexing directory
mkdir kma_indexing
# Index files using kma_index
kma_index -i db_resfinder/fusidicacid.fsa -o db_resfinder/kma_indexing/fusidicacid
kma_index -i db_resfinder/phenicol.fsa -o db_resfinder/kma_indexing/phenicol
kma_index -i db_resfinder/glycopeptide.fsa -o db_resfinder/kma_indexing/glycopeptide
kma_index -i db_resfinder/trimethoprim.fsa -o db_resfinder/kma_indexing/trimethoprim
kma_index -i db_resfinder/oxazolidinone.fsa -o db_resfinder/kma_indexing/oxazolidinone
kma_index -i db_resfinder/tetracycline.fsa -o db_resfinder/kma_indexing/tetracycline
kma_index -i db_resfinder/quinolone.fsa -o db_resfinder/kma_indexing/quinolone
kma_index -i db_resfinder/nitroimidazole.fsa -o db_resfinder/kma_indexing/nitroimidazole
kma_index -i db_resfinder/fosfomycin.fsa -o db_resfinder/kma_indexing/fosfomycin
kma_index -i db_resfinder/aminoglycoside.fsa -o db_resfinder/kma_indexing/aminoglycoside
kma_index -i db_resfinder/macrolide.fsa -o db_resfinder/kma_indexing/macrolide
kma_index -i db_resfinder/sulphonamide.fsa -o db_resfinder/kma_indexing/sulphonamide
kma_index -i db_resfinder/rifampicin.fsa -o db_resfinder/kma_indexing/rifampicin
kma_index -i db_resfinder/colistin.fsa -o db_resfinder/kma_indexing/colistin
kma_index -i db_resfinder/beta-lactam.fsa -o db_resfinder/kma_indexing/beta-lactam

Documentation

The documentation available as of the date of this release can be found at: https://bitbucket.org/genomicepidemiology/resfinder_db/overview.

Citation

When using the method please cite:

Not yet published

License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.