The future of DNA sequence archiving

被引：21

作者：

Cochrane, Guy ^{[1
]}

Cook, Charles E. ^{[1
]}

Birney, Ewan ^{[1
]}

机构：

[1] EMBL Bioinformat Inst, Hinxton CB10 1SD, England

来源：

GIGASCIENCE | 2012年 / 1卷

关键词：

DNA; Sequence; Archive; Compression; Storage; Image;

D O I：

10.1186/2047-217X-1-2

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Archives operating under the International Nucleotide Sequence Database Collaboration currently preserve all submitted sequences equally, but rapid increases in the rate of global sequence production will soon require differentiated treatment of DNA sequences submitted for archiving. Here, we propose a graded system in which the ease of reproduction of a sequencing-based experiment and the relative availability of a sample for resequencing define the level of lossy compression applied to stored data.

引用

页数：5

共 9 条

[1] The Western English Channel contains a persistent microbial seed bank [J].

Caporaso, J. Gregory ;

Paszkiewicz, Konrad ;

Field, Dawn ;

Knight, Rob ;

Gilbert, Jack A. .

ISME JOURNAL, 2012, 6 (06) :1089-1093

[2] TranscriptSNPView: a genome-wide catalog of mouse coding variation [J].

Cunningham, Fiona ;

Rios, Daniel ;

Griffiths, Mark ;

Smith, James ;

Ning, Zemin ;

Cox, Tony ;

Flicek, Paul ;

Marin-Garcin, Pablo ;

Herrero, Javier ;

Rogers, Jane ;

Van der Weyden, Louise ;

Bradley, Allan ;

Birney, Ewan ;

Adams, David J. .

NATURE GENETICS, 2006, 38 (08) :853-853

[3] WHOLE-GENOME RANDOM SEQUENCING AND ASSEMBLY OF HAEMOPHILUS-INFLUENZAE RD [J].

FLEISCHMANN, RD ;

ADAMS, MD ;

WHITE, O ;

CLAYTON, RA ;

KIRKNESS, EF ;

KERLAVAGE, AR ;

BULT, CJ ;

TOMB, JF ;

DOUGHERTY, BA ;

MERRICK, JM ;

MCKENNEY, K ;

SUTTON, G ;

FITZHUGH, W ;

FIELDS, C ;

GOCAYNE, JD ;

SCOTT, J ;

SHIRLEY, R ;

LIU, LI ;

GLODEK, A ;

KELLEY, JM ;

WEIDMAN, JF ;

PHILLIPS, CA ;

SPRIGGS, T ;

HEDBLOM, E ;

COTTON, MD ;

UTTERBACK, TR ;

HANNA, MC ;

NGUYEN, DT ;

SAUDEK, DM ;

BRANDON, RC ;

FINE, LD ;

FRITCHMAN, JL ;

FUHRMANN, JL ;

GEOGHAGEN, NSM ;

GNEHM, CL ;

MCDONALD, LA ;

SMALL, KV ;

FRASER, CM ;

SMITH, HO ;

VENTER, JC .

SCIENCE, 1995, 269 (5223) :496-512

[4] Efficient storage of high throughput DNA sequencing data using reference-based compression [J].

Fritz, Markus Hsi-Yang ;

Leinonen, Rasko ;

Cochrane, Guy ;

Birney, Ewan .

GENOME RESEARCH, 2011, 21 (05) :734-740

[5] The International Nucleotide Sequence Database Collaboration [J].

Karsch-Mizrachi, Ilene ;

Nakamura, Yasukazu ;

Cochrane, Guy .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D33-D37

[6] The sequence read archive: explosive growth of sequencing data [J].

Kodama, Yuichi ;

Shumway, Martin ;

Leinonen, Rasko .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D54-D56

[7] Genomic information infrastructure after the deluge [J].

Parkhill, Julian ;

Birney, Ewan ;

Kersey, Paul .

GENOME BIOLOGY, 2010, 11 (07)

[8] Serendipitous discovery of Wolbachia genomes in multiple Drosophila species -: art. no. R23 [J].

Salzberg, SL ;

Hotopp, JCD ;

Delcher, AL ;

Pop, M ;

Smith, DR ;

Eisen, MB ;

Nelson, WC .

GENOME BIOLOGY, 2005, 6 (03)

[9] NUCLEOTIDE-SEQUENCE OF BACTERIOPHAGE PHICHI174 DNA [J].

SANGER, F ;

AIR, GM ;

BARRELL, BG ;

BROWN, NL ;

COULSON, AR ;

FIDDES, JC ;

HUTCHISON, CA ;

SLOCOMBE, PM ;

SMITH, M .

NATURE, 1977, 265 (5596) :687-695

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