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Protocols

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

 (6)
library_books

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

2013
BMC Bioinformatics
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 into […]

library_books

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

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

[…] raculous 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 are […]

library_books

Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod Independent Photosynthetic Bradyrhizobia

2011
Genes
PMCID: 3899966
PMID: 24704842
DOI: 10.3390/genes3010035

[…] ing errors. Three other genomes were sequenced only with Illumina Solexa technology (STM3847, STM4509 and STM4523) by the company GATC (Germany). Short 36 bp reads were pre-assembled with PERL script Vcake [], using a first round of k-mer extensions of Solexa reads, then a second round using progressive extension of contigs obtained from the first round. This strategy allowed the construction of a […]

library_books

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

2011
PLoS Pathog
PMCID: 3136466
PMID: 21799664
DOI: 10.1371/journal.ppat.1002132

[…] the pipeline described in Reinhardt et al. 2009 . All genomes were subject to all steps of the pipeline downstream of, and including, Newbler assembly. In some cases (Pgy R4, Ppi R6, Pja, Cit7, Ptt) VCAKE was used to build initial contigs from Illumina reads, while in other cases (Pma, Pan, Pla 106, Pla 107, Pmo, Pmp, Pta, Pae, Pac) EDENA was used to build these initial contigs . We found that th […]

library_books

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

2011
PLoS One
PMCID: 3100316
PMID: 21625384
DOI: 10.1371/journal.pone.0019984

[…] y algorithm used by CAP3 , Phrap and TIGR assembler is conceptually the simplest solution to genome assembly and new tools tailored to NGS data have been developed recently like SSAKE , SHARCGS or VCAKE . But maybe the most popular algorithmic solution is the Overlap-Layout-Consensus (OLC) algorithm used in the Celera Assembler , Arachne , , PCAP or Mira to name a few. With the consolidation o […]

call_split

Polyploidy Did Not Predate the Evolution of Nodulation in All Legumes

2010
PLoS One
PMCID: 2905438
PMID: 20661290
DOI: 10.1371/journal.pone.0011630
call_split See protocol

[…] ere removed: sequences consisting of greater than 66% of poly-A -T -G or -C; and sequences with fewer than 30 high quality bases.Contig generation and extension with Illumina sequence proceeded using VCAKE , adding sequences in four batches (to avoid computer memory limitations in the 32 bit perl implementation of VCAKE). Each round used VCAKE parameters -k 42 (i.e. use 42 nucleotides from each se […]

Citations

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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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