CholeraeFinder

===================

This project documents the CholeraeFinder service

Documentation

The CholeraeFinder service contains one python script choleraefinder.py which is the script of the latest version of the CholeraeFinder service. CholeraeFinder identifies important genes in total or partial sequenced isolates of Vibrio Choleraes, and attempts to describe the specimen.

Content of the repository

1. choleraefinder.py - the program
2. README.md
3. Dockerfile - dockerfile for building the choleraefinder docker container

Installation

Setting up CholeraeFinder program
Warning: Due to bugs in BioPython 1.74, if you are not using the Docker container, do not use that version if not using Python 3.7.

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

Build Docker container

# Build container
docker build -t choleraefinder .

#Download and install CholeraeFinder database

# Go to the directory where you want to store the cholearefinder database
cd /path/to/some/dir
# Clone database from git repository
git clone https://bitbucket.org/genomicepidemiology/choleraefinder_db.git
cd choleraefinder_db
CHOLERAE_DB=$(pwd)
# Install CholeraeFinder 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

Usage

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

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

When running the docker file you must mount 2 directories:

1. choleraefinder_db (CholeraeFinder database) downloaded from bitbucket
2. 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 output directory relative to pwd

-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

-tmp temporary directory for storage of the results from the external software

-x extended output: Give extented output with allignment files, template and query hits in fasta and a tab seperated file with gene profile results

-q don't show results

Web-server

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

Citation

When using the method please cite:

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand. Siriphap A, Leekitcharoenphon P, Kaas RS, Theethakaew C, Aarestrup FM, Sutheinkul O, Hendriksen RS. PLoS One. 2017 Jan 19;12(1):e0169324. doi: 10.1371/journal.pone.0169324. eCollection 2017. [Epub ahead of print]

References

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

License

Copyright (c) 2014, Ole Lund, Technical University of Denmark All rights reserved.

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.