Skip Navigation



Bioinformatics Advance Access published online on June 23, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp383
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
25/17/2194    most recent
btp383v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Whiteford, N.
Right arrow Articles by Brown, C.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Whiteford, N.
Right arrow Articles by Brown, C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2009 The Author(s)
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.

Swift: Primary Data Analysis for the Illumina Solexa Sequencing Platform

Nava Whiteford 1,2,*, Tom Skelly 1, Christina Curtis 3, Matt E. Ritchie 4, Andrea Löhr 5, Alexander Wait Zaranek 6, Irina Abnizova 1 and Clive Brown 1,2

1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
2Present Address: Oxford Nanopore Technologies, Begbroke Science Park, Sandy Lane, Kidlington, OX5 1PF, UK
3Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK
4Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
5Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138, USA
6Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA

*To whom correspondence should be addressed. Dr. Nava Whiteford, E-mail: new{at}sgenomics.org, nava.whiteford{at}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 optimisation and validity of their scientific work.]

Results: In this paper 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{at}sgenomics.org

Associate Editor: Dr. Joaquin Dopazo

Received on February 22, 2009; revised on May 4, 2009; accepted on June 18, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.