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

@article{citeulike:4940964, 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. 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. 10.1093/bioinformatics/btp383}, author = {Whiteford, Nava and Skelly, Tom and Curtis, Christina and Ritchie, Matt E. and Lohr, Andrea and Zaranek, Alexander W. and Abnizova, Irina and Brown, Clive}, citeulike-article-id = {4940964}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp383}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/17/2194.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/17/2194.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/17/2194}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19549630}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19549630}, day = {1}, doi = {10.1093/bioinformatics/btp383}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {base-calling, open-source, pipeline, short-read, software, swift, tool}, month = {September}, number = {17}, pages = {2194--2199}, posted-at = {2009-06-26 15:27:58}, priority = {3}, title = {Swift: primary data analysis for the Illumina Solexa sequencing platform}, url = {http://dx.doi.org/10.1093/bioinformatics/btp383}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4940964 L3 - citeulike-article-id:4940964 N2 - 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. 10.1093/bioinformatics/btp383 IS - 17 JF - Bioinformatics SN - 1460-2059 EP - 2199 TI - Swift: primary data analysis for the Illumina Solexa sequencing platform VL - 25 SP - 2194 KW - base-calling KW - open-source KW - pipeline KW - short-read KW - software KW - swift KW - tool AU - Whiteford, Nava AU - Skelly, Tom AU - Curtis, Christina AU - Ritchie, Matt AU - Lohr, Andrea AU - Zaranek, Alexander AU - Abnizova, Irina AU - Brown, Clive PY - 2009/09/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp383 ER -