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VCAKE

Assembles genetic sequences. VCAKE is able to assemble millions of small nucleotide reads even in the presence of sequencing error. It extends the seed sequence one base at a time using the most commonly represented base from these matching reads, provided that the set of reads passes certain conditions. The tool may be a step towards the assembly of larger bacterial genomes from short reads, particularly with the development of superior base calling or paired end technology.

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VCAKE forum

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VCAKE classification

VCAKE specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

VCAKE distribution

versioning

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No versioning.

VCAKE support

Maintainer

  • William Jeck <>

Credits

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Publications

Institution(s)

Department of Biology, University of Carolina—Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Carolina Center for Genome Sciences, University of Carolina—Chapel Hill, Chapel Hill, NC, USA

Funding source(s)

Supported by Carolina Center for Genome Sciences and National Institutes of Health Grant RO1GM066025.

Link to literature

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