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README.md

                      Efficient Referential Genome Compressor (ERGC)
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What is it?

ERGC (Efficient Referential Genome Compressor) is a genome compression tool. It compresses a target genome using a reference genome. It employs a divide and conquer strategy. At first it divides both the target and reference sequences into some parts of equal size and finds one-to-one maps of similar regions from each part. It then outputs identical maps along with dissimilar regions of the target sequence.

Installation

This software package contains two software tools for compressing and decompressing a genomic sequence with respect to a reference. These tools are written in Java Programming Language. These are Utilities.java and DecompressCG.java. To compile the source code please execute "make" command in the package directory.

Instructions

A genomic sequence can be compressed by executing SCRIPT_ERGC_COMP script. Similarly, decompression can be achieved by executing SCRIPT_ERGC_DECOMP script.

Please, follow these instructions to successfully run the tools:

(1) Script should be run in Linux machine.
(2) The machine should have latest JDK (Java Virtual Machine (JVM) 1.6.0 or above).	
(3) The package contains two executables from 7-zip package, i.e., 7za and 7z. Change the access 
    permission of the executables:
    > chmod 777 7za 7z
(4) Change the access permission of the scripts by using chmod command as stated above.
(5) Write the full path of the files in the script. For example in SCRIPT_ERGC_COMP, we have to
    give three file names, i.e., <reference_file_name>, <target_file_name>, and <compressed_file>. 
(6) Run the desired script, i.e., if we want to compress a genomic sequence, execute the following 
    command in a shell within the directory of ERGC: 
    > ./SCRIPT_ERGC_COMP 
(7) The compressed file will be produced with extension 7z, i.e., <compressed_file>.7z. 
(8) In a similar fashion SCRIPT_ERGC_DECOMP can be executed.

Contacts

 o If you have any questions regarding ERGC, please contact Subrata Saha at subrata@csebuet.org

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Efficient Referential Genome Compression Algorithm

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