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Göteborgs universitets publikationer

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

Författare och institution:
Y. Li (-); Hao Wang (Institutionen för biomedicin, avdelningen för infektionssjukdomar); K. Nie (-); C. Zhang (-); Y. Zhang (-); J. Wang (-); P. H. Niu (-); X. J. Ma (-)
Publicerad i:
Scientific Reports, 6 s. Article number: 23774
ISSN:
2045-2322
Publikationstyp:
Artikel, refereegranskad vetenskaplig
Publiceringsår:
2016
Språk:
engelska
Fulltextlänk:
Sammanfattning (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 (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.
Ämne (baseras på Högskoleverkets indelning av forskningsämnen):
MEDICIN OCH HÄLSOVETENSKAP ->
Klinisk medicin
Nyckelord:
generation sequencing data, next-generation, genome sequence, origin, environment, assembler, alignment, software, datasets, velvet
Postens nummer:
236971
Posten skapad:
2016-05-27 10:27
Posten ändrad:
2016-05-30 15:26

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