Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Apr;39(7):e45.
doi: 10.1093/nar/gkr009. Epub 2011 Jan 25.

A novel compression tool for efficient storage of genome resequencing data

Congmao Wang  1 , Dabing Zhang
Affiliations

A novel compression tool for efficient storage of genome resequencing data

Congmao Wang et al. Nucleic Acids Res. 2011 Apr.

Abstract

With the advent of DNA sequencing technologies, more and more reference genome sequences are available for many organisms. Analyzing sequence variation and understanding its biological importance are becoming a major research aim. However, how to store and process the huge amount of eukaryotic genome data, such as those of the human, mouse and rice, has become a challenge to biologists. Currently available bioinformatics tools used to compress genome sequence data have some limitations, such as the requirement of the reference single nucleotide polymorphisms (SNPs) map and information on deletions and insertions. Here, we present a novel compression tool for storing and analyzing Genome ReSequencing data, named GRS. GRS is able to process the genome sequence data without the use of the reference SNPs and other sequence variation information and automatically rebuild the individual genome sequence data using the reference genome sequence. When its performance was tested on the first Korean personal genome sequence data set, GRS was able to achieve ∼159-fold compression, reducing the size of the data from 2986.8 to 18.8 MB. While being tested against the sequencing data from rice and Arabidopsis thaliana, GRS compressed the 361.0 MB rice genome data to 4.4 MB, and the A. thaliana genome data from 115.1 MB to 6.5 KB. This de novo compression tool is available at http://gmdd.shgmo.org/Computational-Biology/GRS.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Architecture of the GRS Tool. The main modules in GRS connect the input chromosome file, the intermediate data and the final compressed file. Details of the processing procedure are described in the text.
Figure 2.
Figure 2.
Processing changes file of DNA base, genome position and recover language. (a) Raw changes between two sequences generated based on the modified UNIX diff program. N1 to N12 indicate the nucleotide sequence position ranging from N1 to N12; ‘a’ is the insertion of nucleotide(s); ‘d’ is the deletion of nucleotide(s) and ‘c’ is the changed nucleotide(s). In addition, symbol ‘,’ between N1 and N2 means positions start from N1 to N2. Symbol ‘>’, ‘<’ and ‘—’ are the keywords when the whole individual genome sequence is rebuilt on basis of the reference genome sequence. (b) Changes file with redundant information deleted. (c) Changes file generated based on the subtracted number, which is more readable to the computer.
Figure 3.
Figure 3.
Method to resolve the minimum varied sequence percentage between the reference and input chromosomes and assemble the pieces together. Here is an example showing that two chromosomes are spliced into nine parts with relevant δi. Part 1, 3, 4, 5, 6, 7 and 8 are put together because δ2 and δ9 with a higher value than others based on the threshold of varied sequence percentage.
See this image and copyright information in PMC

References

    1. Horner DS, Pavesi G, Castrignano T, Meo PDD, Liuni S, Sammeth M, Picardi E, Pesole G. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief. Bioinform. 2009;11:181–197. - PubMed
    1. Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 2009;27:847–852. - PMC - PubMed
    1. Service RF. The race for the $1000 genome. Science. 2006;311:1544–1546. - PubMed
    1. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, et al. The first Korean genome sequence and analysis: Full genome sequencing for asocio-ethnic group. Genome Res. 2009;19:1622–1629. - PMC - PubMed
    1. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen Y, Makhijani V, Roth GT, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008;452:872–876. - PubMed

Publication types