MLST_Kp_linux - Multi-Locus Sequence Typing of Klebsiella pneumoniae  
Welcome to use MLST_Kp_linux local version!
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1. INSTALL MLST_Kp_linux
To install MLST_Kp_linux, just download the file 'MLST_Kp_linux.tar.gz' and then decompress it like this:

$ tar -zxvf MLST_Kp_linux.tar.gz

Before using the MLST_Kp_linux, please ensure that Bioperl has been installed in your server. 
If not, install the Bioperl as well as some other dependent Perl modules by the following command lines
(you need be root or you can use sudo):
# cpan install Bio::SeqIO
# cpan install Bio::SearchIO 

To test and get familiar with the MLST_Kp_linux, you can copy the demo files we provide in the 'example' directory 
to the corresponding location, run `perl run_MLST_Kp_local.pl list_demo.txt`. You can also compare your output 
to the results in the directory 'example/result_demo'.

The local version of MLST_Kp_linux was developed in Linux version 2.6.32-696.10.2.el6.x86_64(Red Hat Enterprise
Linux Server release 6.3). The version of Perl we developed the software is v5.10.1.

2. INPUT DATA
The list file should contain the names of DNA files(FASTA format)in the directory 'MLST_Kp_linux/input' line by line.
List File Format Example
=====
HS11286_chr.fasta
RJA166_chr.fas
RJF293_chr.fna
HS11286_contigs.fasta
KP5-1_chr.fas

3. RUNNING MLST_Kp_linux 
MLST_Kp_linux will start to run immediately by the following command:

$ perl run_MLST_Kp_local.pl list_file

You can check the running status in 'MLST.log'.


4. OUTPUT
The output files with a suffix "_MLST.txt" will be stored in the directory 'MLST_Kp_linux/result'.

Example of output file (HS11286_chr_MLST.txt) 
Strain	ST	gapA	infB	mdh	pgi	phoE	rpoB	tonB
HS11286_chr	ST11	3	3	1	1	1	1	4

If you have any question, please feel free to contact the authors:
hyou@sjtu.edu.cn
xiaobinli@sjtu.edu.cn
