REAPR: a universal tool for genome assembly evaluation

被引：287

作者：

Hunt, Martin ^{[1
]}

Kikuchi, Taisei ^{[1
,2
]}

Sanders, Mandy ^{[1
]}

Newbold, Chris ^{[1
,3
]}

Berriman, Matthew ^{[1
]}

Otto, Thomas D. ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Miyazaki Univ, Fac Med, Dept Infect Dis, Div Parasitol, Miyazaki 8891692, Japan

[3] Univ Oxford, John Radcliffe Hosp, Weatherall Inst Mol Med, Oxford OX3 9DS, England

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 05期

基金：

英国惠康基金;

关键词：

Genome assembly; validation; evaluation; DRAFT ASSEMBLIES; SEQUENCE; ARTEMIS; DNA;

D O I：

10.1186/gb-2013-14-5-r47

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：

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/.

引用

页数：10

共 33 条

[1] Limitations of next-generation genome sequence assembly [J].

Alkan, Can ;

Sajjadian, Saba ;

Eichler, Evan E. .

NATURE METHODS, 2011, 8 (01) :61-65

[2]

[Anonymous], 2010, R LANG ENV STAT COMP

[3] BamTools: a C++ API and toolkit for analyzing and managing BAM files [J].

Barnett, Derek W. ;

Garrison, Erik K. ;

Quinlan, Aaron R. ;

Stroemberg, Michael P. ;

Marth, Gabor T. .

BIOINFORMATICS, 2011, 27 (12) :1691-1692

[4] Toward almost closed genomes with GapFiller [J].

Boetzer, Marten ;

Pirovano, Walter .

GENOME BIOLOGY, 2012, 13 (06)

[5] Scaffolding pre-assembled contigs using SSPACE [J].

Boetzer, Marten ;

Henkel, Christiaan V. ;

Jansen, Hans J. ;

Butler, Derek ;

Pirovano, Walter .

BIOINFORMATICS, 2011, 27 (04) :578-579

[6] Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data [J].

Carver, Tim ;

Harris, Simon R. ;

Berriman, Matthew ;

Parkhill, Julian ;

McQuillan, Jacqueline A. .

BIOINFORMATICS, 2012, 28 (04) :464-469

[7] ACT: the Artemis comparison tool [J].

Carver, TJ ;

Rutherford, KM ;

Berriman, M ;

Rajandream, MA ;

Barrell, BG ;

Parkhill, J .

BIOINFORMATICS, 2005, 21 (16) :3422-3423

[8] Genome Project Standards in a New Era of Sequencing [J].

Chain, P. S. G. ;

Grafham, D. V. ;

Fulton, R. S. ;

FitzGerald, M. G. ;

Hostetler, J. ;

Muzny, D. ;

Ali, J. ;

Birren, B. ;

Bruce, D. C. ;

Buhay, C. ;

Cole, J. R. ;

Ding, Y. ;

Dugan, S. ;

Field, D. ;

Garrity, G. M. ;

Gibbs, R. ;

Graves, T. ;

Han, C. S. ;

Harrison, S. H. ;

Highlander, S. ;

Hugenholtz, P. ;

Khouri, H. M. ;

Kodira, C. D. ;

Kolker, E. ;

Kyrpides, N. C. ;

Lang, D. ;

Lapidus, A. ;

Malfatti, S. A. ;

Markowitz, V. ;

Metha, T. ;

Nelson, K. E. ;

Parkhill, J. ;

Pitluck, S. ;

Qin, X. ;

Read, T. D. ;

Schmutz, J. ;

Sozhamannan, S. ;

Sterk, P. ;

Strausberg, R. L. ;

Sutton, G. ;

Thomson, N. R. ;

Tiedje, J. M. ;

Weinstock, G. ;

Wollam, A. ;

Detter, J. C. .

SCIENCE, 2009, 326 (5950) :236-237

[9] ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies [J].

Clark, Scott C. ;

Egan, Rob ;

Frazier, Peter I. ;

Wang, Zhong .

BIOINFORMATICS, 2013, 29 (04) :435-443

[10] Assemblathon 1: A competitive assessment of de novo short read assembly methods [J].

Earl, Dent ;

Bradnam, Keith ;

St John, John ;

Darling, Aaron ;

Lin, Dawei ;

Fass, Joseph ;

Hung On Ken Yu ;

Buffalo, Vince ;

Zerbino, Daniel R. ;

Diekhans, Mark ;

Ngan Nguyen ;

Ariyaratne, Pramila Nuwantha ;

Sung, Wing-Kin ;

Ning, Zemin ;

Haimel, Matthias ;

Simpson, Jared T. ;

Fonseca, Nuno A. ;

Birol, Inanc ;

Docking, T. Roderick ;

Ho, Isaac Y. ;

Rokhsar, Daniel S. ;

Chikhi, Rayan ;

Lavenier, Dominique ;

Chapuis, Guillaume ;

Naquin, Delphine ;

Maillet, Nicolas ;

Schatz, Michael C. ;

Kelley, David R. ;

Phillippy, Adam M. ;

Koren, Sergey ;

Yang, Shiaw-Pyng ;

Wu, Wei ;

Chou, Wen-Chi ;

Srivastava, Anuj ;

Shaw, Timothy I. ;

Ruby, J. Graham ;

Skewes-Cox, Peter ;

Betegon, Miguel ;

Dimon, Michelle T. ;

Solovyev, Victor ;

Seledtsov, Igor ;

Kosarev, Petr ;

Vorobyev, Denis ;

Ramirez-Gonzalez, Ricardo ;

Leggett, Richard ;

MacLean, Dan ;

Xia, Fangfang ;

Luo, Ruibang ;

Li, Zhenyu ;

Xie, Yinlong .

GENOME RESEARCH, 2011, 21 (12) :2224-2241

← 1 2 3 4 →