Your browser version may not work well with NCBI's Web applications. More information here...
1: Bioinformatics. 2007 Nov 1;23(21):2942-4. Epub 2007 Sep 24.Click here to read Links

Extending assembly of short DNA sequences to handle error.

Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, Jones CD.

Department of Biology, University of Carolina-Chapel Hill, Chapel Hill, NC 27599, USA. william.jeck@gmail.com

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 ( approximately 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

PMID: 17893086 [PubMed - indexed for MEDLINE]