Table of Contents

VCAKE

Overview

VCAKE[1] stands for Verified Consensus Assembly by K-mer Extension.

VCAKE is a de novo short read DNA assembly program that uses ~30mers to assemble genomes. It is geared towards the assembly of Illumina's Solexa sequencing data.[2]

Website

SourceForge project page

Note: The availability link given to the software in the original paper no longer seems to function. Use the SourceForge project page instead.

Source and Documentation

All Files: http://sourceforge.net/projects/vcake/files/

Source (latest version in C): http://sourceforge.net/projects/vcake/files/vcake (c)

Assembly pipeline: http://sourceforge.net/projects/vcake/files/hybrid assembly pipeline/

References

1. a William R. Jeck, Josephine A. Reinhardt, David A. Baltrus, Matthew T. Hickenbotham, Vincent Magrini, Elaine R. Mardis, Jeffery L. Dangl, and Corbin D. Jones. Extending assembly of short DNA sequences to handle error. Bioinformatics 23: 2942-2944. Advance Access published on November 1, 2007, doi:10.1093/bioinformatics/btm451.
2. a http://sourceforge.net/projects/vcake/