Extending assembly of short DNA sequences to handle error.
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.


BACKGROUND
http://152.2.15.114/~labweb/VCAKE
Jeck
William R
WR
Department of Biology, University of Carolina-Chapel Hill, Chapel Hill, NC 27599, USA. william.jeck@gmail.com
Reinhardt
Josephine A
JA
Baltrus
David A
DA
Hickenbotham
Matthew T
MT
Magrini
Vincent
V
Mardis
Elaine R
ER
Dangl
Jeffery L
JL
Jones
Corbin D
CD
D000465:Algorithms; D016477:Artifacts; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016384:Consensus Sequence; D004247:DNA / Q000235:genetics*; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D004247:DNA