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A multi-platform graphical front-end for Velvet. VAGUE aims to make sequence assembly accessible to a wider audience and to facilitate better usage amongst existing users of Velvet.

Software type:
Package
Interface:
Graphical user interface
Restrictions to use:
None
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Computer skills:
Medium
Stability:
Stable
Requirements:
Velvet >= 1.2.07, Java >= 1.6, VelvetK >= 1.0 (optional), Perl >= 5.4 (for VelvetK)
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Maintainer

  • Torsten Seemann <torsten.seemann at monash.edu>

Institution(s)

Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Parkville 3053, Australia

Funding source(s)

This research was supported in part by the Victorian Life Sciences Computation Initiative, an initiative of the Victorian Government hosted by the University of Melbourne, Australia.

  • (Powell and Seemann, 2013) VAGUE: a graphical user interface for the Velvet assembler. Bioinformatics.
    PMID: 23162059
  • (Magoc et al., 2013) GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics.
    PMID: 23665771
  • (Miller et al., 2010) Assembly algorithms for next-generation sequencing data. Genomics.
    PMID: 20211242
  • (Narzisi and Mishra, 2011) Comparing de novo genome assembly: the long and short of it. PloS one.
    PMID: 21559467
  • (Henson et al., 2012) Next-generation sequencing and large genome assemblies. Pharmacogenomics.
    PMID: 22676195
  • (Kleftogiannis et al., 2013) Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PloS one.
    PMID: 24086547
  • (Nagarajan and Pop, 2013) Sequence assembly demystified. Nature reviews Genetics.
    PMID: 23358380
  • (Bradnam et al., 2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience.
    PMID: 23870653
  • (Salzberg et al., 2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome research.
    PMID: 22147368
  • (Utturkar et al., 2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics.
    PMID: 24930142
  • (Alkan et al., 2011) Limitations of next-generation genome sequence assembly. Nature methods.
    PMID: 21102452

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