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Literature DB >> 18604217

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

Yaniv Erlich¹, Partha P Mitra, Melissa delaBastide, W Richard McCombie, Gregory J Hannon.

Abstract

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.

Entities: CellLine Chemical Species

Mesh：

Year: 2008 PMID： 18604217 PMCID： PMC2978646 DOI： 10.1038/nmeth.1230

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

10 in total

Review 1. Emerging technologies in DNA sequencing.

Authors: Michael L Metzker
Journal: Genome Res Date: 2005-12 Impact factor: 9.043

2. Short read fragment assembly of bacterial genomes.

Authors: Mark J Chaisson; Pavel A Pevzner
Journal: Genome Res Date: 2007-12-14 Impact factor: 9.043

3. Breakthrough of the year. Human genetic variation.

Authors: Elizabeth Pennisi
Journal: Science Date: 2007-12-21 Impact factor: 47.728

4. Whole-genome sequencing and variant discovery in C. elegans.

Authors: LaDeana W Hillier; Gabor T Marth; Aaron R Quinlan; David Dooling; Ginger Fewell; Derek Barnett; Paul Fox; Jarret I Glasscock; Matthew Hickenbotham; Weichun Huang; Vincent J Magrini; Ryan J Richt; Sacha N Sander; Donald A Stewart; Michael Stromberg; Eric F Tsung; Todd Wylie; Tim Schedl; Richard K Wilson; Elaine R Mardis
Journal: Nat Methods Date: 2008-01-20 Impact factor: 28.547

5. The year of sequencing.

Authors: Kelly Rae Chi
Journal: Nat Methods Date: 2008-01 Impact factor: 28.547

6. Elimination of residual natural nucleotides from 3'-O-modified-dNTP syntheses by enzymatic mop-up.

Authors: M L Metzker; R Raghavachari; K Burgess; R A Gibbs
Journal: Biotechniques Date: 1998-11 Impact factor: 1.993

7. Paired-end mapping reveals extensive structural variation in the human genome.

Authors: Jan O Korbel; Alexander Eckehart Urban; Jason P Affourtit; Brian Godwin; Fabian Grubert; Jan Fredrik Simons; Philip M Kim; Dean Palejev; Nicholas J Carriero; Lei Du; Bruce E Taillon; Zhoutao Chen; Andrea Tanzer; A C Eugenia Saunders; Jianxiang Chi; Fengtang Yang; Nigel P Carter; Matthew E Hurles; Sherman M Weissman; Timothy T Harkins; Mark B Gerstein; Michael Egholm; Michael Snyder
Journal: Science Date: 2007-09-27 Impact factor: 47.728

8. An analysis of the feasibility of short read sequencing.

Authors: Nava Whiteford; Niall Haslam; Gerald Weber; Adam Prügel-Bennett; Jonathan W Essex; Peter L Roach; Mark Bradley; Cameron Neylon
Journal: Nucleic Acids Res Date: 2005-11-07 Impact factor: 16.971

9. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Authors: Jonathan A Eisen; Robert S Coyne; Martin Wu; Dongying Wu; Mathangi Thiagarajan; Jennifer R Wortman; Jonathan H Badger; Qinghu Ren; Paolo Amedeo; Kristie M Jones; Luke J Tallon; Arthur L Delcher; Steven L Salzberg; Joana C Silva; Brian J Haas; William H Majoros; Maryam Farzad; Jane M Carlton; Roger K Smith; Jyoti Garg; Ronald E Pearlman; Kathleen M Karrer; Lei Sun; Gerard Manning; Nels C Elde; Aaron P Turkewitz; David J Asai; David E Wilkes; Yufeng Wang; Hong Cai; Kathleen Collins; B Andrew Stewart; Suzanne R Lee; Katarzyna Wilamowska; Zasha Weinberg; Walter L Ruzzo; Dorota Wloga; Jacek Gaertig; Joseph Frankel; Che-Chia Tsao; Martin A Gorovsky; Patrick J Keeling; Ross F Waller; Nicola J Patron; J Michael Cherry; Nicholas A Stover; Cynthia J Krieger; Christina del Toro; Hilary F Ryder; Sondra C Williamson; Rebecca A Barbeau; Eileen P Hamilton; Eduardo Orias
Journal: PLoS Biol Date: 2006-09 Impact factor: 8.029

10. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Authors: Shawn J Cokus; Suhua Feng; Xiaoyu Zhang; Zugen Chen; Barry Merriman; Christian D Haudenschild; Sriharsa Pradhan; Stanley F Nelson; Matteo Pellegrini; Steven E Jacobsen
Journal: Nature Date: 2008-02-17 Impact factor: 49.962

10 in total

78 in total

10. Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel.

Authors: Irene Tiemann-Boege; Christina Curtis; Deepali N Shinde; Daniel B Goodman; Simon Tavaré; Norman Arnheim
Journal: Anal Chem Date: 2009-07-15 Impact factor: 6.986

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

Review 1. Emerging technologies in DNA sequencing.

2. Short read fragment assembly of bacterial genomes.

3. Breakthrough of the year. Human genetic variation.

4. Whole-genome sequencing and variant discovery in C. elegans.

5. The year of sequencing.

6. Elimination of residual natural nucleotides from 3'-O-modified-dNTP syntheses by enzymatic mop-up.

7. Paired-end mapping reveals extensive structural variation in the human genome.

8. An analysis of the feasibility of short read sequencing.

9. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

10. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Review 1. Next-generation sequencing in clinical virology: Discovery of new viruses.

2. DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis.

3. Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

4. OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Review 5. Cardiovascular genomics: a biomarker identification pipeline.

6. Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs.

7. BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing.

Review 8. Genomic location analysis by ChIP-Seq.

9. How does inflammation drive mutagenesis in colorectal cancer?

10. Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel.