Skip Navigation


Bioinformatics Advance Access first published online on October 24, 2008
This version published online on October 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn548
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
24/24/2818    most recent
btn548v2
btn548v1
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 Miller, J. R.
Right arrow Articles by Sutton, G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Miller, J. R.
Right arrow Articles by Sutton, G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 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.

Aggressive Assembly of Pyrosequencing Reads with Mates

Jason R. Miller 1,*, Arthur L. Delcher 2, Sergey Koren 1, Eli Venter 1, Brian P. Walenz 1, Anushka Brownley 1, Justin Johnson 1, Kelvin Li 1, Clark Mobarry 3 and Granger Sutton 1

1 The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA
2 Center for Bioinformatics & Computational Biology, University of Maryland, College Park, MD 20742, USA
3 White Oak Technologies Inc, 1300 Spring St.,Ste 320, Silver Spring, MD 20910, USA

*To whom correspondence should be addressed. Dr. Jason R. Miller, E-mail: jmiller{at}jcvi.org


  Abstract

Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length, and the variety of available paired-end protocols. Both read types can complement one another in a "hybrid" approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data.

Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage, and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data.

Availability: The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License.

Contact: jmiller{at}jcvi.org

Link: Online-only supplement.

Associate Editor: Prof. Dmitrij Frishman

Received on June 20, 2008; revised on October 17, 2008; accepted on October 20, 2008

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


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
M. Molla, A. Delcher, S. Sunyaev, C. Cantor, and S. Kasif
Triplet repeat length bias and variation in the human transcriptome
PNAS, October 6, 2009; 106(40): 17095 - 17100.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Assefa, T. M. Keane, T. D. Otto, C. Newbold, and M. Berriman
ABACAS: algorithm-based automatic contiguation of assembled sequences
Bioinformatics, August 1, 2009; 25(15): 1968 - 1969.
[Abstract] [Full Text] [PDF]


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.