Banana Slug Genomics

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====== VCAKE ======

===== Overview =====
VCAKE[(cite:vcake>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:[[http://dx.doi.org/10.1093/bioinformatics/btm451|10.1093/bioinformatics/btm451]].)] stands for **V**erified **C**onsensus **A**ssembly by **K**-mer **E**xtension.

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.[(cite:website>[[http://sourceforge.net/projects/vcake/]])]

==== Website ====
[[http://sourceforge.net/projects/vcake/|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%20%28c%29/|http://sourceforge.net/projects/vcake/files/vcake (c)]]

Assembly pipeline: [[http://sourceforge.net/projects/vcake/files/hybrid%20assembly%20pipeline/|http://sourceforge.net/projects/vcake/files/hybrid assembly pipeline/]]

===== References =====
<refnotes>notes-separator: none</refnotes>
~~REFNOTES cite~~

Banana Slug Genomics

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