Extending assembly of short DNA sequences to handle error.

Published

Journal Article

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.http://152.2.15.114/~labweb/VCAKE

Full Text

Duke Authors

Cited Authors

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

Published Date

  • November 2007

Published In

Volume / Issue

  • 23 / 21

Start / End Page

  • 2942 - 2944

PubMed ID

  • 17893086

Pubmed Central ID

  • 17893086

Electronic International Standard Serial Number (EISSN)

  • 1367-4811

International Standard Serial Number (ISSN)

  • 1367-4803

Digital Object Identifier (DOI)

  • 10.1093/bioinformatics/btm451

Language

  • eng