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

SIM – Analyzing long-range RNA-RNA interactions in Viral Genomes and structured RNAs

SIM

:: DESCRIPTION

SilentMutations (SIM) can analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. It simulates destructive and compensatory mutants of two key regions from a single-stranded RNA, which can then be utilized for the combinatorial in vitro analysis of RNA-RNA interactions.

::DEVELOPER

RNA Bioinformatics and High Throughput Analysis Jena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python
  • numpy
  • viennaRNA

:: DOWNLOAD

SIM

:: MORE INFORMATION

Citation

D. Desiro, M. Hölzer, B. Ibrahim, and M. Marz,
SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs
Virus Res. 2019 Jan 15;260:135-141. doi: 10.1016/j.virusres.2018.11.005. Epub 2018 Nov 12.

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.

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.