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Bioinformatics Advance Access originally published online on September 24, 2007
Bioinformatics 2007 23(21):2942-2944; doi:10.1093/bioinformatics/btm451
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© 2007 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.

Extending assembly of short DNA sequences to handle error

William R. Jeck 1,*, Josephine A. Reinhardt 1, David A. Baltrus 1, Matthew T. Hickenbotham 2, Vincent Magrini 2, Elaine R. Mardis 2, Jeffery L. Dangl 1,3 and Corbin D. Jones 1,3

1Department of Biology, University of Carolina—Chapel Hill, Chapel Hill, NC 27599, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108 and 3Carolina Center for Genome Sciences, University of Carolina—Chapel Hill, Chapel Hill, NC 27599, USA

*To whom correspondence should be addressed.


  Abstract

Inexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illumina's Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (~30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error.

Availability: http://152.2.15.114/~labweb/VCAKE

Contact: william.jeck{at}gmail.com

Associate Editor: Alex Bateman

Received on July 23, 2007; revised on August 21, 2007; accepted on August 24, 2007

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