title: Swift: primary data analysis for the Illumina Solexa sequencing platform.
abstract: BACKGROUND
  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.
authors: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. nava.whiteford@nanoporetech.com
authors: Nava
authors: N
authors: Whiteford
authors: Tom
authors: T
authors: Skelly
authors: Christina
authors: C
authors: Curtis
authors: Matt E
authors: ME
authors: Ritchie
authors: Andrea
authors: A
authors: Löhr
authors: Alexander Wait
authors: AW
authors: Zaranek
authors: Irina
authors: I
authors: Abnizova
authors: Clive
authors: C
authors: Brown
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software