Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Highly curved large-format sensors for infrared imaging.

Optics express·2026

Same author

Ice-binding protein's dual roles for prolonging the enzymatic activity of alcohol dehydrogenase against freezing.

International journal of biological macromolecules·2025

Same author

DRAGoN: a robust pipeline for analyzing DRUG-seq datasets.

Bioinformatics advances·2025

Same author

Colibactin Exerts Androgen-dependent and -independent Effects on Prostate Cancer.

European urology oncology·2024

Same author

Human telomere length is chromosome end-specific and conserved across individuals.

Science (New York, N.Y.)·2024

Same author

Author Correction: Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis.

Nature neuroscience·2023

Same journal

Correction: Bulatov et al. Camelpox Virus in Western Kazakhstan: Assessment of the Role of Local Fauna as Reservoirs of Infection. <i>Viruses</i> 2024, <i>16</i>, 1626.

Viruses·2026

Same journal

Correction: Franco et al. Whole Blood Volume-Based Absolute Quantification of HTLV-1 Proviral Load: A Comparative Method Evaluation Study. <i>Viruses</i> 2026, <i>18</i>, 580.

Viruses·2026

Same journal

Correction: Medkour et al. Adenovirus Infections in African Humans and Wild Non-Human Primates: Great Diversity and Cross-Species Transmission. <i>Viruses</i> 2020, <i>12</i>, 657.

Viruses·2026

Same journal

Burden of Malaria and Dengue Across Global, Asian, and Chinese Populations Based on GBD 2021 Data: A Quantitative Assessment of Importation Risks to China.

Viruses·2026

Same journal

First Report of <i>Orthonairovirus songlingense</i> in <i>Haemaphysalis concinna</i> Ticks from Russia.

Viruses·2026

Same journal

Epidemiological and Virological Characteristics of H9N2 Avian Influenza Virus in Jiangsu Province, China, 2024.

Viruses·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 27, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

MGtree: A Fast and Flexible Alignment-Based Metagenomics Pipeline.

Samantha L Sholes¹, Scott Norton², Alfredo Gonzalez²

¹Department of Data Science & Scientific Informatics, MRL-Information Technology, Merck & Co., Inc., West Point, PA 19486, USA.

|June 26, 2026

Summary

This summary is machine-generated.

MGtree is a new metagenomics pipeline that accurately identifies viral samples using full-length read alignments and phylogenetic analysis. It improves classification precision for complex samples, outperforming existing tools like Kraken2 and Centrifuge.

Keywords:

HPV metagenomics norovirus phylogenetics short read alignment

More Related Videos

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Related Experiment Videos

Last Updated: Jun 27, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Area of Science:

Bioinformatics
Virology
Genomics

Background:

Metagenomics analysis is vital for viral identification and typing in surveillance and clinical settings.
Current methods face limitations in taxonomic resolution and accuracy with complex or recombinant viral samples.

Purpose of the Study:

To introduce MGtree, a novel metagenomics pipeline designed for enhanced viral sample classification.
To evaluate MGtree's performance against existing tools and in challenging sample types.

Main Methods:

MGtree employs a combination of full-length read alignments and phylogenetic analysis for sample classification.
The pipeline was tested on challenging norovirus and human papillomavirus (HPV) datasets, including low-input and coinfected samples.

Main Results:

MGtree accurately genotypes viral samples, demonstrating superior performance compared to Kraken2 and Centrifuge.
The pipeline successfully classifies low-input samples where de novo assembly fails.
MGtree shows high precision in resolving genotypes from highly mutant and coinfected samples.

Conclusions:

MGtree offers improved viral genotype resolution and classification precision, particularly for complex metagenomic samples.
This novel pipeline has the potential to enhance viral surveillance and clinical diagnostics.