Swift: primary data analysis for the Illumina Solexa sequencing platform

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    Author
    Whiteford, N; Skelly, T; Curtis, C; Ritchie, ME; Loehr, A; Zaranek, AW; Abnizova, I; Brown, C
    Date
    2009-09-01
    Source Title
    Bioinformatics
    Publisher
    OXFORD UNIV PRESS
    University of Melbourne Author/s
    Ritchie, Matthew
    Affiliation
    Medical Biology (W.E.H.I.)
    Metadata
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    Document Type
    Journal Article
    Citations
    Whiteford, N., Skelly, T., Curtis, C., Ritchie, M. E., Loehr, A., Zaranek, A. W., Abnizova, I. & Brown, C. (2009). Swift: primary data analysis for the Illumina Solexa sequencing platform. BIOINFORMATICS, 25 (17), pp.2194-2199. https://doi.org/10.1093/bioinformatics/btp383.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/256749
    DOI
    10.1093/bioinformatics/btp383
    Abstract
    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.

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