VIP: an integrated pipeline for metagenomics of virus identification and discovery

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 i...

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Bibliographic Details
Published in:Scientific reports 2016-03, Vol.6 (1), p.23774-23774, Article 23774
Main Authors: Li, Yang, Wang, Hao, Nie, Kai, Zhang, Chen, Zhang, Yi, Wang, Ji, Niu, Peihua, Ma, Xuejun
Format: Article
Language:English
Subjects:
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Algorithms
alignment
Amino acids
assembler
Classification
Clinical Medicine
Computer applications
Data processing
datasets
environment
generation sequencing data
Genes, Viral
genome sequence
High-Throughput Nucleotide Sequencing
Homology
Humanities and Social Sciences
Humans
Identification
Klinisk medicin
Metagenomics
Molecular Typing
multidisciplinary
next-generation
origin
Phylogeny
Public health
Science
Science (multidisciplinary)
Software
Vasoactive intestinal peptide
Velocity
velvet
Viruses - genetics
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Summary: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 .
ISSN:2045-2322
2045-2322
DOI:10.1038/srep23774