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VirFind specifications

Information


Unique identifier OMICS_15198
Name VirFind
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Input format FASTA, FASTQ, SFF
Operating system Windows
Programming languages C++
Computer skills Medium
Version 1.1
Stability No
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ioannis Tzanetakis

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Publication for VirFind

VirFind citations

 (6)
library_books

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

2018
Front Microbiol
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] some workflows require a custom, user-provided database for filtering, providing more flexibility but requiring more user-input. this is seen in imsa (dimon et al., ), virushunter (zhao et al., ), virfind (ho and tzanetakis, ), and metlab (norling et al., ), although other workflows may accept custom references as well. in total, 22 workflows filter non-virus reads prior to further analysis […]

library_books

Novel RNA viruses within plant parasitic cyst nematodes

2018
PLoS One
PMCID: 5839581
PMID: 29509804
DOI: 10.1371/journal.pone.0193881

[…] without rna sequencing technology., the study presented here analyzed nematode transcriptome data to identify and describe novel viral genomes via de novo assembly with the assistance of the virfind toolset (virfind.org) []. nematode species analyzed for viruses in this study include heterodera glycines, h. schachtii, h. avenae, h. trifolli, globodera pallida, g. rostochiensis, g. […]

library_books

Fatal Outbreak in Tonkean Macaques Caused by Possibly Novel Orthopoxvirus, Italy, January 20151

2017
PMCID: 5708245
PMID: 28975882
DOI: 10.3201/eid2312.162098

[…] with qubit dsdna hs assay kit (thermofisher scientific). we prepared dna libraries with the ion xpress plus gdna fragment library kit (thermofisher scientific). we filtered sequence reads with the virfind tool (http://virfind.org/j/) and de novo assembled sequences with newbler version 2.5.3 (454 life sciences, branford, ct, usa). we aligned the 5 major contigs (length 13,743–108,913 nt) […]

library_books

Viral metagenomics of aphids present in bean and maize plots on mixed use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus like dicistrovirus

2017
Virol J
PMCID: 5625602
PMID: 28969654
DOI: 10.1186/s12985-017-0854-x

[…] based on the de bruijn graph algorithm. the resulting contigs from de novo assembly were analysed by blastn against a virus database to detect all viral sequences present in the data. in the virfind online analysis pipeline, the sequences were trimmed (default setting ~5 bases). de novo assembly was performed using trinity (v.2.0.2) but where the average sequence length was ≤80 […]

library_books

An internet based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

2017
BMC Bioinformatics
PMCID: 5225587
PMID: 28077064
DOI: 10.1186/s12859-016-1428-4

[…] novo assembled sequences with similarity to viral genomes., two such automated pipelines have recently been made available, one designed to detect known and novel viruses through de novo assembly [virfind, 11], and the other, limited to extract virnas through mapping onto a priori known viral reference genomes []. virfind is available as a web-based graphical front-end interface, with users […]

library_books

A Next Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity

2016
PLoS One
PMCID: 4795770
PMID: 26986479
DOI: 10.1371/journal.pone.0151495

[…] hpevs have been replicated on the rd99, a549, and vero cell lines, hpev culture is still limited by the low induction of cpe []., to compare current ngs pipelines including virusfinder [] and virfind [], the novelty of the proposed pipeline is to identify unknown pathogens in a mixed clinical sample, and to implement an iterative mapping for generating viral genomes. in terms of viral […]


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VirFind institution(s)
Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA
VirFind funding source(s)
This work was supported by the USDA-APHIS-NCPN (Grant numbers 10-8100-1572, 11-8100-1572).

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