VIRAPOPS 2.1 – Simulates Viral Population from Seed Sequences Family

kGEM (k-Genotype Expectation Maximization algorithm) tool finds haplotypes for Single-amplicon sequencing data. This tool requires aligned reads in special internal format and auxiliary program ERIF could help to convert reads in this format either from fasta (unaligned) format or from SAM (pairwise alignment) format.

::DEVELOPER

Georgia State University NGS Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

kGEM / ERIF

:: MORE INFORMATION

Pooling – Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling

Pooling

:: DESCRIPTION

Pooling is a computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling

::DEVELOPER

Georgia State University NGS Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

Pooling

:: MORE INFORMATION

Citation

Computational Framework for Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling.
Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y.
Bioinformatics. 2014 Oct 29. pii: btu726.

ViralNet – Computing Network Structures in RNA Viral Populations

ViralNet

:: DESCRIPTION

ViralNet is an application for estimating reticulated structures of mixed viral populations.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

ViralNet

:: MORE INFORMATION

Citation

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Donatien Fotso-Chedom, Pablo R. Murcia, Chris D. Greenman
arXiv:1407.7997

AV454 1.0 – de novo Consensus Assembler designed for reads derived from diverse Viral Populations

AV454 1.0

:: DESCRIPTION

AV454 (AssembleViral454) is an assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes. Reads need not be paired, and it is assumed that no sequence repeat in the genome would be large enough to fully contain an average read.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AV454

:: MORE INFORMATION