ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data

Xiaokai Wang; Zhimin Ding; Ying Yang; Lifeng Liang; Yingshuai Sun; Chaojian Hou; Yuning Zheng; Yan Xia; Lixin Dong

doi:10.1099/mgen.0.001202

ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data

Xiaokai Wang (Co-first Author), Zhimin Ding (Co-first Author), Ying Yang, Lifeng Liang, Yingshuai Sun, Chaojian Hou, Yuning Zheng, Yan Xia^*, Lixin Dong^*

^*Corresponding author for this work

Department of Biomedical Engineering

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

6 Citations (Scopus)

23 Downloads (CityUHK Scholars)

Abstract

Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers seeking the most up-to-date tools. To address this, we present ViromeFlowX, a user-friendly Nextflow workflow that automates viral genome assembly, identification, classification, and annotation. This streamlined workflow integrates cutting-edge tools for processing raw sequencing data for taxonomic annotation and functional analysis. Application to a dataset of 200 metagenomic samples yielded high-quality viral genomes. ViromeFlowX enables efficient mining of viral genomic data, offering a valuable resource to investigate the gut virome’s role in virus-host interactions and virus-related diseases. © 2024 The Authors.

Original language	English
Article number	001202
Journal	Microbial Genomics
Volume	10
Issue number	2
Online published	21 Feb 2024
DOIs	https://doi.org/10.1099/mgen.0.001202
Publication status	Published - 2024

Funding

This work was partially supported by the National Natural Science Foundation of China (grant no. 62127810) and the University Grants Committee (project nos. 11213720, 11219419, and 11217221).

Research Keywords

Nextflow-based
Viral Genomes Mining
ViromeFlowX

Publisher's Copyright Statement

This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

RGC Funding Information

RGC-funded

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10.1099/mgen.0.001202

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title = "ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data",

abstract = "Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers seeking the most up-to-date tools. To address this, we present ViromeFlowX, a user-friendly Nextflow workflow that automates viral genome assembly, identification, classification, and annotation. This streamlined workflow integrates cutting-edge tools for processing raw sequencing data for taxonomic annotation and functional analysis. Application to a dataset of 200 metagenomic samples yielded high-quality viral genomes. ViromeFlowX enables efficient mining of viral genomic data, offering a valuable resource to investigate the gut virome{\textquoteright}s role in virus-host interactions and virus-related diseases. {\textcopyright} 2024 The Authors.",

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year = "2024",

doi = "10.1099/mgen.0.001202",

language = "English",

volume = "10",

journal = "Microbial Genomics",

issn = "2057-5858",

publisher = "Microbiology Society",

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ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data. / Wang, Xiaokai (Co-first Author); Ding, Zhimin (Co-first Author); Yang, Ying et al.
In: Microbial Genomics, Vol. 10, No. 2, 001202, 2024.

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

TY - JOUR

T1 - ViromeFlowX

T2 - a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data

AU - Wang, Xiaokai

AU - Ding, Zhimin

AU - Yang, Ying

AU - Liang, Lifeng

AU - Sun, Yingshuai

AU - Hou, Chaojian

AU - Zheng, Yuning

AU - Xia, Yan

AU - Dong, Lixin

PY - 2024

Y1 - 2024

N2 - Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers seeking the most up-to-date tools. To address this, we present ViromeFlowX, a user-friendly Nextflow workflow that automates viral genome assembly, identification, classification, and annotation. This streamlined workflow integrates cutting-edge tools for processing raw sequencing data for taxonomic annotation and functional analysis. Application to a dataset of 200 metagenomic samples yielded high-quality viral genomes. ViromeFlowX enables efficient mining of viral genomic data, offering a valuable resource to investigate the gut virome’s role in virus-host interactions and virus-related diseases. © 2024 The Authors.

AB - Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers seeking the most up-to-date tools. To address this, we present ViromeFlowX, a user-friendly Nextflow workflow that automates viral genome assembly, identification, classification, and annotation. This streamlined workflow integrates cutting-edge tools for processing raw sequencing data for taxonomic annotation and functional analysis. Application to a dataset of 200 metagenomic samples yielded high-quality viral genomes. ViromeFlowX enables efficient mining of viral genomic data, offering a valuable resource to investigate the gut virome’s role in virus-host interactions and virus-related diseases. © 2024 The Authors.

KW - Nextflow-based

KW - Viral Genomes Mining

KW - ViromeFlowX

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DO - 10.1099/mgen.0.001202

M3 - RGC 21 - Publication in refereed journal

C2 - 38381034

SN - 2057-5858

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JO - Microbial Genomics

JF - Microbial Genomics

IS - 2

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ER -

ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data

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GRF: Memoristic Ambient Oxygen Nanosensors for Medical Microrobotic Agents

Cite this

ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data

Abstract

Funding

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

Access Output

Other Access Options

Permanent Link

Other Files and Links

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Projects

GRF: Nanorobotic Manipulation Inside a TEM for In-situ Nanodevice Prototyping and Characterization

GRF: Plasmonic Nanosensors and Antennas for Signal Transduction and Energy Harvesting for Biomedical Microrobots

GRF: Memoristic Ambient Oxygen Nanosensors for Medical Microrobotic Agents

Cite this