TileQC: A system for tile-based quality control of Solexa data

被引：22

作者：

Dolan, Peter C. ^{[1
]}

Denver, Dee R.

机构：

[1] Oregon State Univ, Dept Zool, Corvallis, OR 97331 USA

[2] Oregon State Univ, Ctr Genome Res & Biocomp, Corvallis, OR 97331 USA

来源：

BMC BIOINFORMATICS | 2008年 / 9卷 / 1期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1186/1471-2105-9-250

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Next-generation DNA sequencing technologies such as Illumina's Solexa platform and Roche's 454 approach provide new avenues for investigating genome-scale questions. However, they also present novel analytical challenges that must be met for their effective application to biological questions. Results: Here we report the availability of tileQC, a tile-based quality control system for Solexa data written in the R language. TileQC provides a means of recognizing bias and error in Solexa output by graphically representing data generated by flow cell tiles. The data represented in the images is then made available in the R environment for further analysis and automation of error detection. Conclusion: TileQC offers a highly adaptable and powerful tool for the quality control of Solexa-based DNA sequence data.

引用

页数：10

共 4 条

[1] Whole-genome re-sequencing [J].

Bentley, David R. .

CURRENT OPINION IN GENETICS & DEVELOPMENT, 2006, 16 (06) :545-552

[2] Extending assembly of short DNA sequences to handle error [J].

Jeck, William R. ;

Reinhardt, Josephine A. ;

Baltrus, David A. ;

Hickenbotham, Matthew T. ;

Magrini, Vincent ;

Mardis, Elaine R. ;

Dangl, Jeffery L. ;

Jones, Corbin D. .

BIOINFORMATICS, 2007, 23 (21) :2942-2944

[3] Anticipating the $1,000 genome [J].

Mardis, Elaine R. .

GENOME BIOLOGY, 2006, 7 (07)

[4] Assembling millions of short DNA sequences using SSAKE [J].

Warren, Rene L. ;

Sutton, Granger G. ;

Jones, Steven J. M. ;

Holt, Robert A. .

BIOINFORMATICS, 2007, 23 (04) :500-501

← 1 →