PlasmidFinder

This project documents the PlasmidFinder service

Documentation

The PlasmidFinder service contains one python script plasmidfinder.py which is the script of the latest version of the PlasmidFinder service. The service identifies plasmids in total or partial sequenced isolates of bacteria.

Content of the repository

plasmidfinder.py - the program
test - test folder
README.md
Dockerfile - dockerfile for building the plasmidfinder docker container

Installation

Setting up PlasmidFinder program

# Go to wanted location for plasmidfinder
cd /path/to/some/dir
# Clone and enter the plasmidfinder directory
git clone https://bitbucket.org/genomicepidemiology/plasmidfinder.git
cd plasmidfinder

Build Docker container

# Build container
docker build -t plasmidfinder .
# Run test
docker run --rm -it \
       --entrypoint=/test/test.sh plasmidfinder

#Download and install PlasmidFinder database

# Go to the directory where you want to store the plasmidfinder database
cd /path/to/some/dir
# Clone database from git repository (develop branch)
git clone https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
cd plasmidfinder_db
PLASMID_DB=$(pwd)
# Install PlasmidFinder database with executable kma_index program
python3 INSTALL.py kma_index

If kma_index has no bin install please install kma_index from the kma repository: https://bitbucket.org/genomicepidemiology/kma

Dependencies

In order to run the program without using docker, Python 3.5 (or newer) should be installed along with the following versions of the modules (or newer).

Modules

cgecore 1.5.5
tabulate 0.7.7

Modules can be installed using the following command. Here, the installation of the module cgecore is used as an example:

pip3 install cgecore

KMA and BLAST

Additionally KMA and BLAST version 2.8.1 or newer should be installed. The newest version of KMA and BLAST can be installed from here:

https://bitbucket.org/genomicepidemiology/kma

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

Usage

The program can be invoked with the -h option to get help and more information of the service. Run Docker container:

# Run plasmidfinder container
docker run --rm -it \
       -v $PLASMID_DB:/database \
       -v $(pwd):/workdir \
       plasmidfinder -i [INPUTFILE] -o [OUTDIR] [-d] [-p] [-mp] [-l] [-t]

When running the docker file you have to mount 2 directories:

plasmidfinder_db (PlasmidFinder database) downloaded from bitbucket
An output/input folder from where the input file can be reached and an output files can be saved. Here we mount the current working directory (using $pwd) and use this as the output directory, the input file should be reachable from this directory as well. The path to the infile and outfile directories should be relative to the monuted current working directory.

-i INPUTFILE input file (fasta or fastq) relative to pwd, up to 2 files

-o OUTDIR outpur directory relative to pwd

-d DATABASE set a specific database

-p DATABASE_PATH set path to database, default is /database

-mp METHOD_PATH set path to method (blast or kma)

-l MIN_COV set threshold for minimum coverage

-t THRESHOLD set threshold for mininum blast identity

Web-server

A webserver implementing the methods is available at the CGE website and can be found here: https://cge.cbs.dtu.dk/services/PlasmidFinder/

Citation

When using the method please cite:

PlasmidFinder and pMLST: in silico detection and typing of plasmids. Carattoli A, Zankari E, Garcia-Fernandez A, Volby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H. Antimicrob. Agents Chemother. 2014. April 28th. [Epub ahead of print]

References

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421.
Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307.

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.

kcri-tz/plasmidfinder