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Viral Recombination

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Related Experiment Video

Updated: May 7, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

V-Phaser 2: variant inference for viral populations.

Xiao Yang¹, Patrick Charlebois, Alex Macalalad

¹Broad Institute of MIT & Harvard, 7 Cambridge Center, Cambridge, MA 02142 USA. xiaoyang@broadinstitute.org.

|October 4, 2013

Summary

V-Phaser 2 accurately identifies low-frequency viral variants from deep sequencing data, overcoming challenges in distinguishing true variants from errors. This new software tool enhances viral population studies by improving sensitivity and specificity.

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Area of Science:

Virology
Bioinformatics
Genomics

Background:

Massively parallel sequencing enables ultra-deep coverage of viral genomes.
Distinguishing true low-frequency variants from sequencing errors is a significant challenge.

Purpose of the Study:

To develop and validate V-Phaser 2, a software package for inferring intrahost viral diversity.
To improve the accuracy and efficiency of analyzing ultra-deep sequencing data for viral populations.

Main Methods:

V-Phaser 2 utilizes paired-end read data for phased variant calling.
It incorporates novel strategies for representing and inferring length polymorphisms.
An integrated filter addresses systematic sequencing artifacts to reduce erroneous calls.

Main Results:

V-Phaser 2 accurately infers low-frequency intrahost variants from ultra-deep sequencing data.
The software demonstrated superior sensitivity and specificity compared to existing tools (QuRe, V-Phaser).
V-Phaser 2 achieved this performance with significantly reduced computational time and memory usage.

Conclusions:

V-Phaser 2 is a publicly available software tool for analyzing ultra-deep sequencing data of viral populations.
It efficiently processes data from common next-generation sequencing platforms.
The tool facilitates accurate inference of viral intrahost diversity.