TITLE

VAGUE: a graphical user interface for the Velvet assembler

AUTHOR(S)
Powell, David R.; Seemann, Torsten
PUB. DATE
January 2013
SOURCE
Bioinformatics;Jan2013, Vol. 29 Issue 2, p264
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Summary: Velvet is a popular open-source de novo genome assembly software tool, which is run from the Unix command line. Most of the problems experienced by new users of Velvet revolve around constructing syntactically and semantically correct command lines, getting input files into acceptable formats and assessing the output. Here, we present Velvet Assembler Graphical User Environment (VAGUE), 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.Availability and implementation: VAGUE is implemented in JRuby and targets the Java Virtual Machine. It is available under an open-source GPLv2 licence from http://www.vicbioinformatics.com/.Contact: torsten.seemann@monash.edu
ACCESSION #
85098692

 

Related Articles

  • MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. Chun Liang; Feng Sun; Haiming Wang; Junfeng Qu; Freeman Jr, Robert M; Pratt, Lee H; Cordonnier-Pratt, Marie-Mich&x00E8;le // BMC Bioinformatics;2006, Vol. 7, p115 

    Background: Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the...

  • WEKA--Experiences with a Java Open-Source Project. Bouckaert, Remco R.; Frank, Eibe; Hall, Mark A.; Holmes, Geoffrey; Pfahringer, Bernhard; Reutemann, Peter; H.Witten, Ian // Journal of Machine Learning Research;9/1/2010, Vol. 11 Issue 9, p2533 

    No abstract available.

  • Poweliks malware hides in your Registry, not your drive. CONSTANTIN, LUCIAN // PCWorld;Oct2014, Vol. 32 Issue 10, p35 

    The article explains how malware program Poweliks which runs from the Windows Registry and remains fileless thereby avoiding detection. Topics covered include infection and creation of startup Registry entry, JavaScript code, and Windows PowerShell script. It mentions the rogue dynamic link...

  • JColorGrid: software for the visualization of biological measurements. Joachimiak, Marcin P; Weisman, Jennifer L; May, Barnaby CH // BMC Bioinformatics;2006, Vol. 7, p225 

    Background: Two-dimensional data colourings are an effective medium by which to represent three-dimensional data in two dimensions. Such "color-grid" representations have found increasing use in the biological sciences (e.g. microarray 'heat maps' and bioactivity data) as they are particularly...

  • ABC: software for interactive browsing of genomic multiple sequence alignment data. Cooper, Gregory M.; Singaravelu, Senthil A. G.; Sidow, Arend // BMC Bioinformatics;2004, Vol. 5, p192 

    Background: Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring the inclusion of genomic multiple sequence alignments, sequence annotations, and scores describing regional...

  • KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. Sacomoto, Gustavo A. T.; Kielbassa, Janice; Chikhi, Rayan; Uricaru, Raluca; Antoniou, Pavlos; Sagot, Marie-France; Peterlongo, Pierre; Lacroix, Vincent // BMC Bioinformatics;2012 Supplement 6, Vol. 13 Issue Suppl 6, p1 

    Background: In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn...

  • Modeling For Runtime Locality Optimizations of Distributed Java Applications Using Dynamic Localization Algorithm. Verma, Daya Shankar; Kumar, Abhay; Chakrabarty, Amarto; Banka, Haider; Priyam, Amrita // International Journal of Advanced Computer Research;Mar2013, Vol. 3 Issue 1, p91 

    In distributed java environments the locality of objects plays a crucial role in determining the performance, scalability and stability of the overall system. A manual distribution of objects has several drawbacks and requires a series of assumptions which may not be applicable as the system...

  • Implementing JAVA based Virtual Machine for Embedding Wireless Sensor Network Nodes. Rathod, Jayesh N.; Agrawal, Rashmi S. // International Journal of Advanced Research in Computer Science;Jul2011, Vol. 2 Issue 4, p209 

    On the design of a reliable programming model for wireless sensor networks (WSN), we must deal with various concerns, such as heterogeneousness of sensors, different sensing capabilities, dynamic updates and power consumption. The adhoc-networking characteristic of WSNs, its nonviable physical...

  • Azul could become a ray of light for Sun.  // MarketWatch: Technology;Jan2007, Vol. 6 Issue 1, p16 

    The article focuses on the advantages of the Vega 1 Compute Appliances from Azul Systems Inc. in the U.S. The introduction of the devices marked the entry of the concept of network-attached processing. The company claims that the devices are designed to support Java applications. Specifically,...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics