ArticleScientific reports2016
VIP: an integrated pipeline for metagenomics of virus identification and discovery.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Mining viruses in public databases unveils the diversity within the Deltaflexiviridae family.Archives of virology · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- ViromeXplore: integrative workflows for complete and reproducible virome characterization.Briefings in bioinformatics · 2025Article
- Development of Immunodetection Systems Using a Specific Antibody Against the Recombinant Coat Protein for Detecting Sugarcane Streak Mosaic Virus.Pathogens (Basel, Switzerland) · 2025Article
- Gut virome: New key players in the pathogenesis of inflammatory bowel disease.World journal of methodology · 2025Review
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling.BMC bioinformatics · 2024Article
- Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence.Neural regeneration research · 2024Review
- Benchmarking informatics approaches for virus discovery: caution is needed when combiningmSystems · 2024Article
- Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples.bioRxiv : the preprint server for biology · 2024Article
- A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Hecatomb: an integrated software platform for viral metagenomics.GigaScience · 2024Article
- CAPTVRED: an automated pipeline for viral tracking and discovery from capture-based metagenomics samples.Bioinformatics advances · 2024Article
- Article
- Enhanced Viral Metagenomics with Lazypipe 2.Viruses · 2023Article
- Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Long-term host-pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of recent retroviral introgression.Virus evolution · 2023Article
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- Cervical Microbiome in Women Infected with HPV16 and High-Risk HPVs.International journal of environmental research and public health · 2022Article
- Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification and discovery of viruses using next-generation sequencing technology is a fast-developing area with potential wide application in clinical diagnostics, public health monitoring and novel virus discovery. However, tremendous sequence data from NGS study has posed great challenge both in accuracy and velocity for application of NGS study. Here we describe VIP ("Virus Identification Pipeline"), a one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (~10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time. VIP is released under GPLv3 and is available for free download at: https://github.com/keylabivdc/VIP.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.