Alta-Cyclic: a selfoptimizing base caller for next-generation sequencing

被引：135

作者：

Erlich, Yaniv ^{[1
,2
]}

Mitra, Partha P. ^{[1
]}

delaBastide, Melissa ^{[1
]}

McCombie, W. Richard ^{[1
]}

Hannon, Gregory J. ^{[1
,2
]}

机构：

[1] Cold Spring Harbor Lab, Watson Sch Biol Sci, Cold Spring Harbor, NY 11724 USA

[2] Cold Spring Harbor Lab, Howard Hughes Med Inst, Cold Spring Harbor, NY 11724 USA

来源：

NATURE METHODS | 2008年 / 5卷 / 08期

关键词：

D O I：

10.1038/nmeth.1230

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Next-generation sequencing is limited to short read lengths and by high error rates. We systematically analyzed sources of noise in the Illumina Genome Analyzer that contribute to these high error rates and developed a base caller, Alta-Cyclic, that uses machine learning to compensate for noise factors. Alta-Cyclic substantially improved the number of accurate reads for sequencing runs up to 78 bases and reduced systematic biases, facilitating confident identification of sequence variants.

引用

页码：679 / 682

页数：4

共 10 条

[1] Short read fragment assembly of bacterial genomes [J].

Chaisson, Mark J. ;

Pevzner, Pavel A. .

GENOME RESEARCH, 2008, 18 (02) :324-330

[2] The year of sequencing [J].

Chi, Kelly Rae .

NATURE METHODS, 2008, 5 (01) :11-14

[3] Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning [J].

Cokus, Shawn J. ;

Feng, Suhua ;

Zhang, Xiaoyu ;

Chen, Zugen ;

Merriman, Barry ;

Haudenschild, Christian D. ;

Pradhan, Sriharsa ;

Nelson, Stanley F. ;

Pellegrini, Matteo ;

Jacobsen, Steven E. .

NATURE, 2008, 452 (7184) :215-219

[4] Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote [J].

Eisen, Jonathan A. ;

Coyne, Robert S. ;

Wu, Martin ;

Wu, Dongying ;

Thiagarajan, Mathangi ;

Wortman, Jennifer R. ;

Badger, Jonathan H. ;

Ren, Qinghu ;

Amedeo, Paolo ;

Jones, Kristie M. ;

Tallon, Luke J. ;

Delcher, Arthur L. ;

Salzberg, Steven L. ;

Silva, Joana C. ;

Haas, Brian J. ;

Majoros, William H. ;

Farzad, Maryam ;

Carlton, Jane M. ;

Smith, Roger K., Jr. ;

Garg, Jyoti ;

Pearlman, Ronald E. ;

Karrer, Kathleen M. ;

Sun, Lei ;

Manning, Gerard ;

Elde, Nels C. ;

Turkewitz, Aaron P. ;

Asai, David J. ;

Wilkes, David E. ;

Wang, Yufeng ;

Cai, Hong ;

Collins, Kathleen ;

Stewart, Andrew ;

Lee, Suzanne R. ;

Wilamowska, Katarzyna ;

Weinberg, Zasha ;

Ruzzo, Walter L. ;

Wloga, Dorota ;

Gaertig, Jacek ;

Frankel, Joseph ;

Tsao, Che-Chia ;

Gorovsky, Martin A. ;

Keeling, Patrick J. ;

Waller, Ross F. ;

Patron, Nicola J. ;

Cherry, J. Michael ;

Stover, Nicholas A. ;

Krieger, Cynthia J. ;

del Toro, Christina ;

Ryder, Hilary F. ;

Williamson, Sondra C. .

PLOS BIOLOGY, 2006, 4 (09) :1620-1642

[5] Whole-genome sequencing and variant discovery in C-elegans [J].

Hillier, LaDeana W. ;

Marth, Gabor T. ;

Quinlan, Aaron R. ;

Dooling, David ;

Fewell, Ginger ;

Barnett, Derek ;

Fox, Paul ;

Glasscock, Jarret I. ;

Hickenbotham, Matthew ;

Huang, Weichun ;

Magrini, Vincent J. ;

Richt, Ryan J. ;

Sander, Sacha N. ;

Stewart, Donald A. ;

Stromberg, Michael ;

Tsung, Eric F. ;

Wylie, Todd ;

Schedl, Tim ;

Wilson, Richard K. ;

Mardis, Elaine R. .

NATURE METHODS, 2008, 5 (02) :183-188

[6]

Korbel JO, 2007, SCIENCE, V318, P420, DOI 10.1126/science.1149504

[7] Emerging technologies in DNA sequencing [J].

Metzker, ML .

GENOME RESEARCH, 2005, 15 (12) :1767-1776

[8] Elimination of residual natural nucleotides from 3′-O-modified-dNTP syntheses by enzymatic mop-up [J].

Metzker, ML ;

Raghavachari, R ;

Burgess, K ;

Gibbs, RA .

BIOTECHNIQUES, 1998, 25 (05) :814-817

[9] Breakthrough of the year - Human genetic variation [J].

Pennisi, Elizabeth .

SCIENCE, 2007, 318 (5858) :1842-1843

[10] An analysis of the feasibility of short read sequencing -: art. no. E171 [J].

Whiteford, N ;

Haslam, N ;

Weber, G ;

Prügel-Bennett, A ;

Essex, JW ;

Roach, PL ;

Bradley, M ;

Neylon, C .

NUCLEIC ACIDS RESEARCH, 2005, 33 (19) :1-6

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