VirFind protocols

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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 No

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Publication for VirFind

VirFind in pipelines

 (2)
2018
PMCID: 5839581
PMID: 29509804
DOI: 10.1371/journal.pone.0193881

[…] primers listed in . nucleotide sequences were translated and aligned with geneious version 9.1.7 (biomatters) using clustalw (blosum cost matrix, gap open cost of 10, gap extend cost of 0.1)., virfind [] (virfind.org) analysis of cyst nematode transcriptomes identified three novel viral genomes. the names and ncbi genbank accession numbers for the nematode viruses identified in this report […]

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

[…] sanger institute []. g. rostochiensis (pcn) female rnaseq data (illumina hiseq 2000) are available from the university of dundee (err1173512)., rna sequencing fastq files were uploaded onto the virfind server [] (virfind.org). blastx and blastn e-values were set at 1.0e-2 with no trimming of contigs. de novo assembled contigs were uploaded into geneious version 9.1.7 (biomatters, auckland, […]


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VirFind in publications

 (6)
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 […]

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. […]

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) […]

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 […]

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 […]


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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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