GRS - A novel compression tool for efficient storage of Genome Re-Sequencing data

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Updates

(These are the major updates only, for all revisions, see HISTORY.txt)

December 10, 2010 - GRS 1.0 is online. GRS 1.0 changed quite a lot to improve user experiences.

November 1, 2010 - GRS 1.0.0 is online.

About

With the advent of DNA sequencing technologies, more and more reference genome sequences for many organisms are available. Analyzing sequence variation and understanding its biological importance are becoming a major research aim. While, how to store and process the huge eukaryotic genome data such as the human, mouse and rice etc., is a challenging question for biologists. Current available bioinformatics tools compressing genomic sequence data require the deduced data of reference Single Nucleotide Polymorphisms (SNPs) map and deletion and insertion DNA information. Here, we present a novel compression tool named GRS for storing and analyzing Genome Re-Sequencing data. GRS is able to process the genome sequence data without the requirement of reference SNPs and other variants. In addition, GRS can automatically re-build the individual genome sequence data using the reference genome sequence. The performance of GRS was tested on the set of first Korean personal genome sequence data with 2986.80 MB in size, which was reduced to 18.8 MB by GRS, with about 159 fold compression level. Furthermore, the utility of GRS was tested for the sequencing data of rice and Arabidopsis thaliana, i.e. 361 MB for rice genome was compressed to 4.4 MB, and 115.10 MB of Arabidopsis thaliana genome to 6.5 KB.

Author

GRS is written and maintained by Congmao Wang, who is a member of the Zhang Lab.

License

Anyone can use the source codes, documents or the excutable file of GRS free of charge for non-commercial use. For commercial use, please contact the author.

Download

GRS1.0 Source Code

GRS1.0 64-bit (X86_64, Ubuntu)

GRS1.0 64-bit (X86_64, Fedora)

GRS1.0 32-bit (X86, Ubuntu)

GRS1.0 32-bit (X86, Centos)

Example File

Feedback

Comments, suggestions, questions, bug reports, etc, are all very welcomed. For all the enquiries, please send to springwang@sjtu.edu.cn.


(Last modified on December 10, 2010 03:10 AM)