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Bioinformatics. 2009 Sep 1;25(17):2194-9. doi: 10.1093/bioinformatics/btp383. Epub 2009 Jun 23.

Swift: primary data analysis for the Illumina Solexa sequencing platform.

Author information

1
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. nava.whiteford@nanoporetech.com

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.

PMID:
19549630
PMCID:
PMC2734321
DOI:
10.1093/bioinformatics/btp383
[Indexed for MEDLINE]
Free PMC Article

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