VirAmp – Galaxy-based Viral Genome Assembly pipeline

VirAmp

:: DESCRIPTION

VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. VirAmp is a collection of existing tools, combined into a single Galaxy interface. Users without further computational knowledge can easily operate the pipeline.

::DEVELOPER

Szpara Laboratory

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

VirAmp: a galaxy-based viral genome assembly pipeline.
Wan Y, Renner DW, Albert I, Szpara ML.
Gigascience. 2015 Apr 28;4:19. doi: 10.1186/s13742-015-0060-y.

MosaicSolver – Determining Recombinants of Viral Genomes from Pileup data

MosaicSolver

:: DESCRIPTION

MosaicSolver determines the recombinants originating from two parent genomes, and their proportions, using next-generation sequencing pileup data.

::DEVELOPER

The Warwick Systems Biology Centre (WSB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • MatLab

:: DOWNLOAD

  MosaicSolver

:: MORE INFORMATION

Citation

Graham R. Wood, Eugene V. Ryabov, Jessica M. Fannon, Jonathan D. Moore, David J. Evans and Nigel Burroughs (2014).
MosaicSolver: a tool for determining recombinants of viral genomes from pileup data.
Nucleic Acids Research (2014) doi:10.1093/nar/gku524

VGA v1 – Viral Genome Assembler

VGA v1

:: DESCRIPTION

VGA is a method for accurate assembly of a heterogeneous viral population consisting of individuals viral genomes (also known as quasi-species).

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Python
  • C++ Compiler

:: DOWNLOAD

 VGA

:: MORE INFORMATION

Citation:

Accurate viral population assembly from ultra-deep sequencing data.
Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E.
Bioinformatics. 2014 Jun 15;30(12):i329-i337. doi: 10.1093/bioinformatics/btu295.

VGO 3.1 – Viral Genome Browser

VGO 3.1

:: DESCRIPTION

VGO (Viral Genome Organizer) is an easy-to-use Java genome browser.  It can be used to display information about a genome, including its genes, ORFs and start/stop codons. It can also be used to perform a regular expression search, a fuzzy motif search, and a masslist search. Because VGO talks to our database of genome sequences (VOCs) it can be used to compare genomes.

::DEVELOPER

the Upton lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

VGO

:: MORE INFORMATION

Citation:

Lefkowitz, E. J., Upton, C., Changayil, S. S., Buck, C., Traktman, P., Buller, R. M. L. 2005.
Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. Nucleic Acids Res. 2005 33: p. D311-D316

C. Upton, D. Hogg, D. Perrin, M. Boone and N. Harris, 2001.
Viral Genome Organizer: A system for analyzing complete viral genomes. Virus Research 70, 55-64.

PriSM – Primer Selection and Matching for Amplification of Viral Genomes

PriSM

:: DESCRIPTION

PriSM is a set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ (2011)
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.
Bioinformatics 27(2): 266-267.