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Updated: Jun 23, 2025

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
Published on: March 11, 2020
Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and
Worakorn Phumiphanjarphak1,2, Pakorn Aiewsakun3,4
1Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, 272 Rama VI Road, Bangkok, 10400, Thailand.
Entourage is a new bioinformatics software that simplifies virus detection and analysis from complex metagenomic next-generation sequencing data. It enables comprehensive virome investigation, even for novel viruses, with ease of use.
Area of Science:
- Bioinformatics
- Virology
- Genomics
Background:
- Pan-virus detection is challenging due to conserved genetic element variability.
- Metagenomic next-generation sequencing (mNGS) offers unbiased virome analysis but involves complex data processing.
- Efficient bioinformatics tools are crucial for effective virome investigation using mNGS.
Purpose of the Study:
- To develop a streamlined bioinformatics software, Entourage, for comprehensive virome investigation.
- To address the complexity of mNGS data analysis for virus detection.
- To provide an all-in-one solution for end-to-end viral sequence analysis.
Main Methods:
- Entourage integrates short-read sequence assembly, viral sequence searching (reference-based and reference-free), and intrasample variation quantification.
- Workflows facilitate end-to-end analysis from read cleaning to virus sequence searching via a single command line.
- The software was tested on simulated data from virus-spiked HeLa cell cultures and a real-world Tara Oceans dataset.
Main Results:
- Entourage enables efficient virus detection, including novel viruses, even with low sequencing depth (single digits).
- The software accurately quantifies intrasample virus genetic variations, demonstrated using SARS-CoV-2 data.
- Comprehensive results facilitate quality control, reliability assessment, and interpretation of virome data.
Conclusions:
- Entourage is a versatile and user-friendly bioinformatics software for virome investigation.
- It streamlines complex mNGS data analysis for virus detection and characterization.
- Entourage is available as open-source software under the MIT license.
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