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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

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Influenza sequence validation and annotation using VADR.

Vincent C Calhoun¹, Eneida L Hatcher¹, Linda Yankie¹

¹National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, United States.

Biorxiv : the Preprint Server for Biology

|May 7, 2024

Summary

A new tool, VADR, now offers standalone influenza sequence validation and annotation, improving upon the existing FLAN system. VADR provides accurate results and supports a wider range of influenza sequences.

Keywords:

annotation influenza

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High-throughput Detection Method for Influenza Virus

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High-throughput Detection Method for Influenza Virus

High-throughput Detection Method for Influenza Virus

Published on: February 4, 2012

Area of Science:

Virology
Bioinformatics
Genomics

Background:

GenBank receives thousands of influenza sequences annually.
FLAN, a webserver tool, has validated and annotated these sequences since 2007 but lacks standalone functionality.
VADR is a standalone tool used for other viral sequence processing.

Approach:

Developed VADR influenza models using FLAN reference sequences.
Adapted VADR for accurate influenza sequence annotation.
Compared VADR performance against FLAN.

Key Points:

VADR and FLAN demonstrate consistent results for most influenza sequences.
VADR often corrects discrepancies where FLAN is incorrect.
VADR successfully annotates influenza D and novel influenza A subtypes (H17-H19, N10-N11) that FLAN cannot process.

Conclusions:

VADR provides a robust, standalone alternative for influenza sequence validation and annotation.
VADR enhances the processing of diverse influenza virus sequences.
VADR 1.6.3 and its influenza models are now publicly available for download and use.