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Items: 1 to 20 of 139

1.

Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

Ewing B, Hillier L, Wendl MC, Green P.

Genome Res. 1998 Mar;8(3):175-85.

2.
3.

preAssemble: a tool for automatic sequencer trace data processing.

Adzhubei AA, Laerdahl JK, Vlasova AV.

BMC Bioinformatics. 2006 Jan 17;7:22.

4.

Adjust quality scores from alignment and improve sequencing accuracy.

Li M, Nordborg M, Li LM.

Nucleic Acids Res. 2004 Sep 30;32(17):5183-91. Print 2004.

5.

Consed: a graphical tool for sequence finishing.

Gordon D, Abajian C, Green P.

Genome Res. 1998 Mar;8(3):195-202.

6.

Quality scores and SNP detection in sequencing-by-synthesis systems.

Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):763-70. doi: 10.1101/gr.070227.107. Epub 2008 Jan 22.

7.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

8.

An automated film reader for DNA sequencing based on homomorphic deconvolution.

Ives JT, Gesteland RF, Stockham TG Jr.

IEEE Trans Biomed Eng. 1994 Jun;41(6):509-19.

PMID:
7927370
9.

RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

Shibata K, Itoh M, Aizawa K, Nagaoka S, Sasaki N, Carninci P, Konno H, Akiyama J, Nishi K, Kitsunai T, Tashiro H, Itoh M, Sumi N, Ishii Y, Nakamura S, Hazama M, Nishine T, Harada A, Yamamoto R, Matsumoto H, Sakaguchi S, Ikegami T, Kashiwagi K, Fujiwake S, Inoue K, Togawa Y.

Genome Res. 2000 Nov;10(11):1757-71.

10.

A general approach to the analysis of errors and failure modes in the base-calling function in automated fluorescent DNA sequencing.

Izmailov A, Goloubentzev D, Jin C, Sunay S, Wisco V, Yager TD.

Electrophoresis. 2002 Aug;23(16):2720-8.

PMID:
12210177
11.

A maximum-likelihood base caller for DNA sequencing.

Brady D, Kocic M, Miller AW, Karger BL.

IEEE Trans Biomed Eng. 2000 Sep;47(9):1271-80.

PMID:
11008429
12.

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA.

Science. 2010 Jan 1;327(5961):78-81. doi: 10.1126/science.1181498. Epub 2009 Nov 5.

13.

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

Menges F, Narzisi G, Mishra B.

Bioinformatics. 2011 Sep 1;27(17):2330-7. doi: 10.1093/bioinformatics/btr393. Epub 2011 Jun 30.

PMID:
21724593
14.

Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences.

Prosdocimi F, Lopes DA, Peixoto FC, Mourão MM, Pacífico LG, Ribeiro RA, Ortega JM.

Genet Mol Res. 2007 Oct 5;6(4):756-65.

15.

ESTprep: preprocessing cDNA sequence reads.

Scheetz TE, Trivedi N, Roberts CA, Kucaba T, Berger B, Robinson NL, Birkett CL, Gavin AJ, O'Leary B, Braun TA, Bonaldo MF, Robinson JP, Sheffield VC, Soares MB, Casavant TL.

Bioinformatics. 2003 Jul 22;19(11):1318-24.

PMID:
12874042
16.

Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values.

Prosdocimi F, Peixoto FC, Ortega JM.

Genet Mol Res. 2004 Dec 30;3(4):483-92.

17.
18.

Automation for genomics, part one: preparation for sequencing.

Meldrum D.

Genome Res. 2000 Aug;10(8):1081-92. Review.

19.

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

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.

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