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Introduction

[General Usage]

[Getting Started]

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Introduction

VirHap is an open-source software package for viral quasi-species reconstruction, which makes use of a
novel phyloprobabilistic approach to infer the sub clonal composition and evolutionary history of a viral population from NGS data. The program aims to characterize and quantify the composition, the abundance and the evolutionary path of the underlying viral population within a given host by analyzing Next Generation Sequencing data.

VirHap takes as input the collection of reads (or several collections of reads in case of many data samples or daily data) and the reference genome and it constructs the evolutionary tree exhibiting the species abundance profile and the list of haplotypes along with their prevalences.
That viral quasispecies reconstruction has three phases (see fig. 1), each having several steps or modules.
They are :

1. Reads processing

2. Mutations computation

3. Quasispecies Reconstruction

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Project Members:

• Donatien Chedom Fotso (admin)