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

Artikel i vetenskaplig tidskrift
Författare Y. Li
Hao Wang
K. Nie
C. Zhang
Y. Zhang
J. Wang
P. H. Niu
X. J. Ma
Publicerad i Scientific Reports
Volym 6
Sidor Article number: 23774
ISSN 2045-2322
Publiceringsår 2016
Publicerad vid Institutionen för biomedicin, avdelningen för infektionssjukdomar
Sidor Article number: 23774
Språk en
Länkar dx.doi.org/10.1038/srep23774
Ämnesord generation sequencing data, next-generation, genome sequence, origin, environment, assembler, alignment, software, datasets, velvet
Ämneskategorier Klinisk medicin

Sammanfattning

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 (similar to 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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