Assisted assembly: how to improve a de novo genome assembly by using related species

被引：32

作者：

Gnerre, Sante ^{[1
]}

Lander, Eric S. ^{[1
]}

Lindblad-Toh, Kerstin ^{[1
,2
]}

Jaffe, David B. ^{[1
]}

机构：

[1] Harvard & MIT, Broad Inst, Cambridge Ctr, Cambridge, MA 02142 USA

[2] Uppsala Univ, Dept Med Biochem & Microbiol, S-75123 Uppsala, Sweden

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 08期

关键词：

PLASMODIUM-FALCIPARUM; SEQUENCE; ARACHNE;

D O I：

10.1186/gb-2009-10-8-r88

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly.

引用

页数：9

共 17 条

[1]

Batzoglou S, 2002, GENOME RES, V12, P177, DOI 10.1101/gr.208902

[2]

*BROAD I, ASS ASS

[3]

*BROAD I, COMP RES DEV

[4] Genome sequence of the human malaria parasite Plasmodium falciparum [J].

Gardner, MJ ;

Hall, N ;

Fung, E ;

White, O ;

Berriman, M ;

Hyman, RW ;

Carlton, JM ;

Pain, A ;

Nelson, KE ;

Bowman, S ;

Paulsen, IT ;

James, K ;

Eisen, JA ;

Rutherford, K ;

Salzberg, SL ;

Craig, A ;

Kyes, S ;

Chan, MS ;

Nene, V ;

Shallom, SJ ;

Suh, B ;

Peterson, J ;

Angiuoli, S ;

Pertea, M ;

Allen, J ;

Selengut, J ;

Haft, D ;

Mather, MW ;

Vaidya, AB ;

Martin, DMA ;

Fairlamb, AH ;

Fraunholz, MJ ;

Roos, DS ;

Ralph, SA ;

McFadden, GI ;

Cummings, LM ;

Subramanian, GM ;

Mungall, C ;

Venter, JC ;

Carucci, DJ ;

Hoffman, SL ;

Newbold, C ;

Davis, RW ;

Fraser, CM ;

Barrell, B .

NATURE, 2002, 419 (6906) :498-511

[5] Whole-genome sequence assembly for mammalian genomes: Arachne 2 [J].

Jaffe, DB ;

Butler, J ;

Gnerre, S ;

Mauceli, E ;

Lindblad-Toh, K ;

Mesirov, JP ;

Zody, MC ;

Lander, ES .

GENOME RESEARCH, 2003, 13 (01) :91-96

[6]

LANDER E S, 1988, Genomics, V2, P231

[7] Genome sequence, comparative analysis and haplotype structure of the domestic dog [J].

Lindblad-Toh, K ;

Wade, CM ;

Mikkelsen, TS ;

Karlsson, EK ;

Jaffe, DB ;

Kamal, M ;

Clamp, M ;

Chang, JL ;

Kulbokas, EJ ;

Zody, MC ;

Mauceli, E ;

Xie, XH ;

Breen, M ;

Wayne, RK ;

Ostrander, EA ;

Ponting, CP ;

Galibert, F ;

Smith, DR ;

deJong, PJ ;

Kirkness, E ;

Alvarez, P ;

Biagi, T ;

Brockman, W ;

Butler, J ;

Chin, CW ;

Cook, A ;

Cuff, J ;

Daly, MJ ;

DeCaprio, D ;

Gnerre, S ;

Grabherr, M ;

Kellis, M ;

Kleber, M ;

Bardeleben, C ;

Goodstadt, L ;

Heger, A ;

Hitte, C ;

Kim, L ;

Koepfli, KP ;

Parker, HG ;

Pollinger, JP ;

Searle, SMJ ;

Sutter, NB ;

Thomas, R ;

Webber, C ;

Lander, ES .

NATURE, 2005, 438 (7069) :803-819

[8] Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes [J].

Margulies, EH ;

Maduro, VVB ;

Thomas, PJ ;

Tomkins, JP ;

Amemiya, CT ;

Luo, MZ ;

Green, ED .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (09) :3354-3359

[9] Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences [J].

Mikkelsen, Tarjei S. ;

Wakefield, Matthew J. ;

Aken, Bronwen ;

Amemiya, Chris T. ;

Chang, Jean L. ;

Duke, Shannon ;

Garber, Manuel ;

Gentles, Andrew J. ;

Goodstadt, Leo ;

Heger, Andreas ;

Jurka, Jerzy ;

Kamal, Michael ;

Mauceli, Evan ;

Searle, Stephen M. J. ;

Sharpe, Ted ;

Baker, Michelle L. ;

Batzer, Mark A. ;

Benos, Panayiotis V. ;

Belov, Katherine ;

Clamp, Michele ;

Cook, April ;

Cuff, James ;

Das, Radhika ;

Davidow, Lance ;

Deakin, Janine E. ;

Fazzari, Melissa J. ;

Glass, Jacob L. ;

Grabherr, Manfred ;

Greally, John M. ;

Gu, Wanjun ;

Hore, Timothy A. ;

Huttley, Gavin A. ;

Kleber, Michael ;

Jirtle, Randy L. ;

Koina, Edda ;

Lee, Jeannie T. ;

Mahony, Shaun ;

Marra, Marco A. ;

Miller, Robert D. ;

Nicholls, Robert D. ;

Oda, Mayumi ;

Papenfuss, Anthony T. ;

Parra, Zuly E. ;

Pollock, David D. ;

Ray, David A. ;

Schein, Jacqueline E. ;

Speed, Terence P. ;

Thompson, Katherine ;

VandeBerg, John L. ;

Wade, Claire M. .

NATURE, 2007, 447 (7141) :167-U1

[10] Scaffolding and validation of bacterial genome assemblies using optical restriction maps [J].

Nagarajan, Niranjan ;

Read, Timothy D. ;

Pop, Mihai .

BIOINFORMATICS, 2008, 24 (10) :1229-1235

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