Journal Article

Swift: primary data analysis for the Illumina Solexa sequencing platform

Nava Whiteford, Tom Skelly, Christina Curtis, Matt E. Ritchie, Andrea Löhr, Alexander Wait Zaranek, Irina Abnizova and Clive Brown

in Bioinformatics

Volume 25, issue 17, pages 2194-2199
Published in print September 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp383

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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.

Availability and Implementation: Swift is implemented in C++and supported under Linux. It is supplied under an open source license (LGPL3), allowing researchers to build upon the platform. Swift is available from http://swiftng.sourceforge.net.

Contact: new@sgenomics.org; nava.whiteford@nanoporetech.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4925 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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