Swift: primary data analysis for the Illumina Solexa sequencing platform

被引：61

作者：

Whiteford, Nava ^{[1
]}

Skelly, Tom ^{[1
]}

Curtis, Christina ^{[2
]}

Ritchie, Matt E. ^{[3
]}

Loehr, Andrea ^{[4
]}

Zaranek, Alexander Wait ^{[5
]}

Abnizova, Irina ^{[1
]}

Brown, Clive ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Univ Cambridge, CRUK Cambridge Res Inst, Li Ka Shing Ctr, Dept Oncol, Cambridge CB2 0RE, England

[3] Walter & Eliza Hall Inst Med Res, Bioinformat Div, Parkville, Vic 3052, Australia

[4] Harvard Smithsonian Ctr Astrophys, Cambridge, MA 02138 USA

[5] Harvard Univ, Sch Med, Boston, MA 02115 USA

来源：

BIOINFORMATICS | 2009年 / 25卷 / 17期

基金：

英国惠康基金;

关键词：

D O I：

10.1093/bioinformatics/btp383

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Primary data analysis methods are of critical importance in second generation DNA sequencing. Improved methods have the potential to increase yield and reduce the error rates. Openly documented analysis tools enable the user to understand the primary data, this is important for the optimization and validity of their scientific work. Results: In this article, we describe Swift, a new tool for performing primary data analysis on the Illumina Solexa Sequencing Platform. Swift is the first tool, outside of the vendors own software, which completes the full analysis process, from raw images through to base calls. As such it provides an alternative to, and independent validation of, the vendor supplied tool. Our results show that Swift is able to increase yield by 13.8%, at comparable error rate.

引用

页码：2194 / 2199

页数：6

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