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A Platform for Epidemiological Investigation and Comparative Genomic Analysis
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sample_run/contigFiles
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README.md
sample_run.sh

README.md

cano-wgMLST files

  1. Open Virtualization Format file: cano-wgMLST.ova.7z (5.2 GB)
  2. The source file: cano-wgMLST.7z (3 MB)
  3. README file: README.md (5 KB)
  4. Results of C. jejuni: C.jejuni.7z (59 MB)

How to run

  1. run with VirtualBox or VMware

    Use VirtualBox (https://www.virtualbox.org) or VMware (http://www.vmware.com) to import "cano-wgMLST.ova". The root password is 'rootwgmlst', the normal user (wgmlst) password is 'wgmlst'.

     $ 7za x cano-wgMLST.ova.7z
    

    or

  2. install cano-wgMLST (cano-wgMLST.7z)

    To install all related tools, and use Perl and Python scripts to run.

    ###Installation###

     Use CentOS 7.4.1708 as OS to show how to install.
    
     $ 7za x cano-wgMLST.7z
     $ cd cano-wgMLST
    
     * set PATH
     	setenv PATH /YOUR_DIR/cano-wgMLST:/YOUR_DIR/cano-wgMLST/bin:$PATH
    

    ###Software required###

     Following is a list of the softwares that you need:
    
     * Perl v5.16.3 (https://www.perl.org)
     * Python 2.7.5 (https://www.python.org)
     * Prokka v1.13 (https://github.com/tseemann/prokka)
     * Roary v3.12.0 (https://github.com/sanger-pathogens/Roary)
     * R v3.5.0 (https://www.r-project.org)
     * Fastx-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/download.html)
     * PHYLIP v3.696 (http://evolution.genetics.washington.edu/phylip.html)
     * pip (https://pypi.org/project/pip/)
     	$ wget https://bootstrap.pypa.io/get-pip.py
     	$ python get-pip.py
     * ETE3-Toolkit (http://etetoolkit.org)
     	$ sudo pip install ete3
     * scikit-learn (http://scikit-learn.org/stable/)
     	$ sudo pip install -U scikit-learn
     * pdftk
     	$ sudo yum localinstall https://www.linuxglobal.com/static/blog/pdftk-2.02-1.el7.x86_64.rpm
     * xvfb-run
     	$ sudo yum install xorg-x11-server-Xvfb
     * IPython
     	$ sudo yum install python-devel.x86_64 python27-python-devel.x86_64 gcc
     	$ sudo pip install ipython
    

Command details

Run sample_run.sh

$ sample_run.sh
	Usage:
		sample_run.sh input_contigs_dir output_dir number_of_threads
	Arguments:
		Input contig directory [String]
		Output directory [String]
		Number of threads [Integer]
	Example: 
		Perform sample run by using 12 threads
		sample_run.sh ./sample_run/contigFiles ./sample_run 12

Run 1.Contig-Annotator.pl

$ 1.Contig-Annotator.pl
	Usage:
		1.Contig-Annotator.pl -i input_dir -o output_dir [-p number_of_threads]
	Arguments:
		-i  Input contig directory [String]
		-o  Output annotated contig directory [String]
		-p  Number of threads [Integer]  Optional
		  default = 1
	Example: 
		Generate annotated contig files using 12 threads
		1.Contig-Annotator.pl -i ./contigFiles -o ./1.contigAnn -p 12

Run 2.PGAdb-Builder.pl

$ 2.PGAdb-Builder.pl 
	Usage:
		2.PGAdb-Builder.pl -i input_dir -o output_dir [-m min_identity] [-p number_of_threads]
	Arguments:
		-i  Input cintig annotated directory [String]
		-o  Output PGAdb directory [String]
		-m  Minimum percentage identity for blastp [Integer]  Optional
		  default = 95
		-p  Number of threads [Integer]  Optional
		  default = 1
	Example: 
		Generate PGAdb using 12 threads
		2.PGAdb-Builder.pl -i ./1.contigAnn -o ./2.PGAdb -p 12

Run 3.wgMLST-Profiler.pl

$ 3.wgMLST-Profiler.pl 
	Usage:
	3.wgMLST-Profiler.pl -i input_dir -d profileDB_dir -o output_dir [-m align_identity] [-n align_coverage] [-p number_of_threads] [-s scheme_file]
	Arguments:
		-i  Input contig directory [String]
		-d  Input PGAdb directory [String]
		-o  Output wgProfiles directory [String]
		-m  Percentage of aligned identity for blastn [Integer]  Optional
		  default = 90
		-n  Aligned coverage for blastn [Real]  Optional
		  default = 0.9
		-p  Number of threads [Integer]  Optional
		  default = 1
		-s  Selected scheme file [String]  Optional
	Example:
		Generate whole genome profiles using 12 threads
		3.wgMLST-Profiler.pl -i ./contigFiles -d ./2.PGAdb -o ./3.wgProfiles -p 12

Run 4.Dendro-Plotter.pl

$ 4.Dendro-Plotter.pl 
	Usage:
		4.Dendro-Plotter.pl -i input_dir -o output_dir [-s scheme_file]
	Arguments:
		-i  Input wgProfiles directory [String]
		-o  Output dendrogram directory [String]
		-s  Selected scheme file [String]  Optional
		  default = 'input_dir/scheme/core.scheme'
	Example:
		Dendro-Plotter with core scheme
		4.Dendro-Plotter.pl -i ./3.wgProfiles -o ./4.DendroPlot

Run 5.Loci-Extractor.pl

$ 5.Loci-Extractor.pl
	Usage:
		5.Loci-Extractor.pl -i input_dir -o output_dir -s scheme_file [-t top_threshold]
	Arguments:
		-i  Input dendrogram directory [String]
		-o  Output extracted loci directory [String]
		-s  Selected scheme file [String]  Optional
		  default = 'input_dir/core.scheme'
		-t  Top threshold [Integer]  Optional
		  default = 5
	Example: 
		Loci-Extractor
		5.Loci-Extractor.pl -i ./4.DendroPlot -o ./5.ExtractedLoci 
Date: 2019/07/29
Author:	Yen-Yi Liu (current788@gmail.com),
	Ji-Wei Lin (jwlin@imst.nsysu.edu.tw),
	Chih-Chieh Chen (chieh@imst.nsysu.edu.tw)

This work has been published in Frontiers in Microbiology 2019.

YY Liu†, JW Lin† and CC Chen* (2019) cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis. Front. Microbiol. 10:1687. doi: 10.3389/fmicb.2019.01687

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