QSdpR

This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population.

Features

Quasispecies
mRNA virus
Clustering
Semidefinite program
HIV-1 virus

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Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

Programming Language

C, Python, Unix Shell

Related Categories

Unix Shell Bio-Informatics Software, Python Bio-Informatics Software, C Bio-Informatics Software

Registered

2016-05-16

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