In Silico E. Coli serotyping tool

Licence: GNU General Public License v3.0 (copy provided in directory)
Author: Tom van Wijk
Contact: tom_van_wijk@hotmail.com

DESCRIPTION

Blast-based tool for in silico serotyping of e. coli assemblies. The reference database used for typing is a blast database created using the database of serotypefinder from CGE (Center for Genomic Epidemiology). When using this tool, please also cite the authors of that database as:

Joensen, K. G., A. M. Tetzschner, A. Iguchi, F. M. Aarestrup, and F. Scheutz. 2015. Rapid and easy in silico serotyping of Escherichia coli using whole genome sequencing (WGS) data. J.Clin.Microbiol. 53(8):2410-2426. doi:JCM.00008-15 [pii];10.1128/JCM.00008-15 [doi]

DOCKER

You may execute this program in a docker container using the provided Dockerfile. In this case, follow these instructions, otherwise continue to the next section.

The docker image is based on the multi_serotyper.py therefore it can process one or more FASTA files at the same time

Instructions to build and run the docker container:

• Clone the ecoli_serotyper repository to the desired location on your system.
  git clone https://github.com/Papos92/ecoli_serotyper.git
• Build the docker image running the following command inside the location in which you downloaded the repo. This may take a short while and requires internet access.
  docker build -t serotyper .
• Run the image, you pass the input FASTA files with the -v argument. For that you must put all your input FASTA files inside a folder which will be the first part of the -v argument, and then keep the second part of the argument as is: :/app/data. When finished you'll see the console output of the multi_serotyper.py program.
  docker run -ti -v /input_data/fasta_files:/app/data serotyper:latest

REQUIREMENTS

• Linux operating system. This software is developed on Linux Ubuntu v16.04
  WARNING: Experiences when using different operating systems may vary.
• python v2.7.x
• python libraries as listed in the import section of ecoli_serotyper.py
• Blast v2.6.0+
• The reference directory supplied with this repository contaning the H-database and O-database

INSTALLATION

• Clone the ecoli_serotyper repository to the desired location on your system.
  git clone https://github.com/Papos92/ecoli_serotyper.git
• Add the location of the ecoli_serotyper directory to the PATH variable:
  export PATH=$PATH:/path/to/ecoli_serotyper.py
  (It is recommended to add this command to your ~/.bashrc file)
• Create path variable ECOLI_REF to the reference subdirectory:
  export SERO_REF=/path/to/ecoli_serotyper/reference
  (It is recommended to add this command to your ~/.bashrc file)

USAGE

Start ecoli_serotyper.py with the following command:

ecoli_serotyper.py -i 'inputfile' -o 'outputdir'

• 'inputfile': location of input file.
  This should be a fully assembled genome in .fasta/.fsa/.fna/.fa format.

• 'outputdir': location of output directory.
  If none is specified, an output directory will be created in the directory containing the inputfile.

Multi Serotyper

Added in this repository is multi_serotyper.py. This script allows for large batches of data to be typed with a single command. When the installation of ecoli_serotyper is complete, no additional dependencies have to be installed and no additional steps have to be taken, you are ready to go.

This script will create an output directory with a subdirectory for each genome containing the ecoli_serotyper.py output. Additionally multy_serotyper_output.txt will be created with an overview of all typed genomes.

USAGE

Start multi_serotyper with the following command:

multi_serotyper.py -i 'inputdir' -o 'outputdir'

• 'inputdir': location of input directory.
  This should only contain fully assembled genomes in .fasta/.fsa/.fna/.fa format.

• 'outputdir': location of output directory.
  If none is specified, an output directory will be created in input directory.