Acceleration of short and long DNA read mapping without loss of accuracy using suffix array

被引：12

作者：

Tarraga, Joaquin ^{[1
,2
]}

Arnau, Vicente ^{[3
]}

Martinez, Hector ^{[4
]}

Moreno, Raul ^{[5
]}

Cazorla, Diego ^{[5
]}

Salavert-Torres, Jose ^{[6
]}

Blanquer-Espert, Ignacio ^{[6
,7
]}

Dopazo, Joaquin ^{[1
,2
,8
]}

Medina, Ignacio ^{[1
]}

机构：

[1] INB CIPF, Ctr Invest Principe Felipe, Dept Computat Genom, Valencia 46012, Spain

[2] INB CIPF, Valencia 46012, Spain

[3] Univ Valencia, Dept Informat, E-46100 Valencia, Spain

[4] Univ Jaume 1, Dept Ingn & Ciencia Comp, Castellon De La Plana 12071, Spain

[5] Univ Castilla La Mancha, Inst Invest Informat Albacete, Albacete 02071, Spain

[6] Univ Politecn Valencia, Inst Instrumentac Imagen Mol, Valencia 46022, Spain

[7] La Fe Polytech Univ Hosp, Grp Invest Biomed Imagen GIBI 2 30, Valencia 46022, Spain

[8] CIBER Enfermedades Raras CIBERER, Bioinformat Rare Dis BIER, Valencia, Spain

来源：

BIOINFORMATICS | 2014年 / 30卷 / 23期

关键词：

DATABASE SEARCHES; ALIGNMENT;

D O I：

10.1093/bioinformatics/btu553

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20x for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.

引用

页码：3396 / 3398

页数：3

共 15 条

[1]

[Anonymous], SIAM J COMPUT

[2] Exome sequencing makes medical genomics a reality [J].

Biesecker, Leslie G. .

NATURE GENETICS, 2010, 42 (01) :13-14

[3] BlastR-fast and accurate database searches for non-coding RNAs [J].

Bussotti, Giovanni ;

Raineri, Emanuele ;

Erb, Ionas ;

Zytnicki, Matthias ;

Wilm, Andreas ;

Beaudoing, Emmanuel ;

Bucher, Philipp ;

Notredame, Cedric .

NUCLEIC ACIDS RESEARCH, 2011, 39 (16) :6886-6895

[4] Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory [J].

Chaisson, Mark J. ;

Tesler, Glenn .

BMC BIOINFORMATICS, 2012, 13

[5] CGAP-Align: A High Performance DNA Short Read Alignment Tool [J].

Chen, Yaoliang ;

Hong, Ji ;

Cui, Wanyun ;

Zaneveld, Jacques ;

Wang, Wei ;

Gibbs, Richard ;

Xiao, Yanghua ;

Chen, Rui .

PLOS ONE, 2013, 8 (04)

[6] STAR: ultrafast universal RNA-seq aligner [J].

Dobin, Alexander ;

Davis, Carrie A. ;

Schlesinger, Felix ;

Drenkow, Jorg ;

Zaleski, Chris ;

Jha, Sonali ;

Batut, Philippe ;

Chaisson, Mark ;

Gingeras, Thomas R. .

BIOINFORMATICS, 2013, 29 (01) :15-21

[7] Tools for mapping high-throughput sequencing data [J].

Fonseca, Nuno A. ;

Rung, Johan ;

Brazma, Alvis ;

Marioni, John C. .

BIOINFORMATICS, 2012, 28 (24) :3169-3177

[8]

Langmead B, 2012, NAT METHODS, V9, P357, DOI [10.1038/NMETH.1923, 10.1038/nmeth.1923]

[9]

Li H., 2013, ARXIV, DOI DOI 10.48550/ARXIV.1303.3997

[10] SOAP3: ultra-fast GPU-based parallel alignment tool for short reads [J].

Liu, Chi-Man ;

Wong, Thomas ;

Wu, Edward ;

Luo, Ruibang ;

Yiu, Siu-Ming ;

Li, Yingrui ;

Wang, Bingqiang ;

Yu, Chang ;

Chu, Xiaowen ;

Zhao, Kaiyong ;

Li, Ruiqiang ;

Lam, Tak-Wah .

BIOINFORMATICS, 2012, 28 (06) :878-879

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