VCAKE

UNLABELLED: 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

Extending assembly of short DNA sequences to handle error.

VCAKE is a tool for short read-based genome assembly using a modification of simple k-mer extension method and it accounts for sequencing error by taking advantage of high read coverage.  It is a modification of the assembler SSAKE.

VCAKE

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