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VCAKE specifications

Information


Unique identifier OMICS_00037
Name VCAKE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline William Jeck <>

Publication for VCAKE

VCAKE citations

 (14)
library_books

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

2016
PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] (l) of all the reads and their overlaps information is then constructed as a graph and (3) the consensus (c) sequence is finally inferred from the graph. software packages such as ssake, sharcgs, vcake, celera assembler, arachne, and pcap take the olc approach [,,,,,]., a de bruijn graph assembly is based on k-mer graphs from the input reads. the nodes of the graph are constituted […]

library_books

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next generation sequencing data

2015
PMCID: 4402509
PMID: 25586223
DOI: 10.1093/nar/gkv002

[…] new microbial genomes with polymerase chain recation., many assemblers have been recently categorized in a review by miller et al. (). one school of assemblers such as amos (), cap3 (), celera (), vcake () and newbler () use traditional olconsensus (olc) algorithms which identify overlaps between various long reads and subsequently merge the read fragments into longer sequences. this approach […]

library_books

A base composition analysis of natural patterns for the preprocessing of metagenome sequences

2013
PMCID: 3816298
PMID: 24564274
DOI: 10.1186/1471-2105-14-S11-S5

[…] using approaches from probability theory, or from the memory-based, are gaining popularity. this was determined by zhang et. al. [] who compared the performance of eight distinct tools (i.e., ssake, vcake, qsra, sharcgs, edena, velvet, soapdenovo, and taipan) against eight groups of simulated datasets., in metagenomic studies, where there are different kinds of reads or contigs mixed together […]

library_books

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

2013
PMCID: 3625192
PMID: 23593174
DOI: 10.1371/journal.pone.0060204

[…] idba-ud and abyss . even though we have selected these five assemblers for this study, there are several other excellent assembly algorithms such as allpaths lg , celera , ray , ssake and vcake that are available for assembling genomes. the five algorithms we have used in this study were selected because velvet, soapdenovo and abyss are widely used, whereas meraculous and idba-ud […]

library_books

Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen

2012
PMCID: 3396655
PMID: 22808161
DOI: 10.1371/journal.pone.0040430

[…] a read length of 76 bp and 64,726,030 paired reads with a read length of 100 bp, respectively, were obtained., the solexa reads were then trimmed according to their quality and assembled using the vcake assembly pipeline (version 1.1). in all, 2,817,877 contigs, with a total base of 429 mb, were obtained. the n50 of the assembly was 140 bp and the largest contig 18,366 bp. the generated […]

library_books

Footprint of Positive Selection in Treponema pallidum subsp. pallidum Genome Sequences Suggests Adaptive Microevolution of the Syphilis Pathogen

2012
PMCID: 3373638
PMID: 22720110
DOI: 10.1371/journal.pntd.0001698

[…] reference. regions in the reference-guided assembled genome where maq could not resolve sequence were then compared to contiguous sequences assembled through the use of the de novo assembly software vcake , and a single contiguous draft sequence was then produced. nucleotide differences between matched pairs were identified using the diffseq program from the emboss software suite. the locations […]


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VCAKE 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
VCAKE funding source(s)
Supported by Carolina Center for Genome Sciences and National Institutes of Health Grant RO1GM066025.

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