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Swift: primary data analysis for the Illumina Solexa sequencing platform
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 optim...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734321/ https://www.ncbi.nlm.nih.gov/pubmed/19549630 http://dx.doi.org/10.1093/bioinformatics/btp383 |
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author | Whiteford, Nava Skelly, Tom Curtis, Christina Ritchie, Matt E. Löhr, Andrea Zaranek, Alexander Wait Abnizova, Irina Brown, Clive |
author_facet | Whiteford, Nava Skelly, Tom Curtis, Christina Ritchie, Matt E. Löhr, Andrea Zaranek, Alexander Wait Abnizova, Irina Brown, Clive |
author_sort | Whiteford, Nava |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2734321 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-27343212009-08-31 Swift: primary data analysis for the Illumina Solexa sequencing platform Whiteford, Nava Skelly, Tom Curtis, Christina Ritchie, Matt E. Löhr, Andrea Zaranek, Alexander Wait Abnizova, Irina Brown, Clive Bioinformatics Original Papers 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. Oxford University Press 2009-09-01 2009-06-23 /pmc/articles/PMC2734321/ /pubmed/19549630 http://dx.doi.org/10.1093/bioinformatics/btp383 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Whiteford, Nava Skelly, Tom Curtis, Christina Ritchie, Matt E. Löhr, Andrea Zaranek, Alexander Wait Abnizova, Irina Brown, Clive Swift: primary data analysis for the Illumina Solexa sequencing platform |
title | Swift: primary data analysis for the Illumina Solexa sequencing platform |
title_full | Swift: primary data analysis for the Illumina Solexa sequencing platform |
title_fullStr | Swift: primary data analysis for the Illumina Solexa sequencing platform |
title_full_unstemmed | Swift: primary data analysis for the Illumina Solexa sequencing platform |
title_short | Swift: primary data analysis for the Illumina Solexa sequencing platform |
title_sort | swift: primary data analysis for the illumina solexa sequencing platform |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734321/ https://www.ncbi.nlm.nih.gov/pubmed/19549630 http://dx.doi.org/10.1093/bioinformatics/btp383 |
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