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

Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, Zaranek AW, Abnizova I, Brown C - Bioinformatics (2009)

Bottom Line: Improved methods have the potential to increase yield and reduce the error rates.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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Related in: MedlinePlus

Pairwise intensity plots from cycle 1 of a Genome Analyzer 2 run after crosstalk correction.
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Figure 3: Pairwise intensity plots from cycle 1 of a Genome Analyzer 2 run after crosstalk correction.

Mentions: Some Genome Analyzer datasets produce deviations in crosstalk, which appear intensity dependent. This produces slightly ‘bowed’ plots as seen in Figure 2. Placing a linear regression though the minimal values produces poor results and we therefore adopt a second strategy in addition to the method described to cope with this scenario. In this method, we identify a set of clusters (using the chastity metric described below) where it is likely that the correct base call can easily be determined, and then perform a linear regression on these values and derive a correction matrix as before. Figure 3 shows the pairwise intensity plots after correction.Fig. 3.


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

Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, Zaranek AW, Abnizova I, Brown C - Bioinformatics (2009)

Pairwise intensity plots from cycle 1 of a Genome Analyzer 2 run after crosstalk correction.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2734321&req=5

Figure 3: Pairwise intensity plots from cycle 1 of a Genome Analyzer 2 run after crosstalk correction.
Mentions: Some Genome Analyzer datasets produce deviations in crosstalk, which appear intensity dependent. This produces slightly ‘bowed’ plots as seen in Figure 2. Placing a linear regression though the minimal values produces poor results and we therefore adopt a second strategy in addition to the method described to cope with this scenario. In this method, we identify a set of clusters (using the chastity metric described below) where it is likely that the correct base call can easily be determined, and then perform a linear regression on these values and derive a correction matrix as before. Figure 3 shows the pairwise intensity plots after correction.Fig. 3.

Bottom Line: Improved methods have the potential to increase yield and reduce the error rates.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH
Related in: MedlinePlus