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VirusFinder specifications

Information


Unique identifier OMICS_00226
Name VirusFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some sequences from a host, a reference host genome, and a reference virus genome.
Input format FASTQ, FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 2.0
Stability No
Requirements
BASH, shell, Java
Maintained No

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Publications for VirusFinder

VirusFinder in publications

 (6)
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] grouping reads according to their respective taxa before assembly. assembly improvement by taxonomic clustering is exemplified in five workflows: metavir (roux et al., ), rins (bhaduri et al., ), virusfinder (wang et al., ), surpi (in comprehensive mode) (naccache et al., ), and vip (li et al., ). two of the discussed workflows have multiple iterations of assembly and combine algorithms […]

PMCID: 5719570
PMID: 29212479
DOI: 10.1186/s12916-017-0973-7

[…] shown in additional file : table s1. additional rnaseq dataset from chiu et al. [] with 16 paired hccs and non-tumorous livers (sra id: srp062885) were also used for pathogenic snp load analysis., virusfinder is an automated virus-host integration detection software package that can deal with virus-induced host genome instability and viral genome variability [, ]. it has been shown […]

PMCID: 5468335
PMID: 28607437
DOI: 10.1038/s41598-017-03508-z

[…] (sinv-1, sinv-2, sinv-3, fex-1, iapv, dwv, kbv, bqcv, abpv, chronic bee paralysis virus (cbpv), varroa destructor virus 1 (vdv-1) and sacbrood virus) using bowtie 2 and to all known viruses using virusfinder. to determine whether we had contamination we also mapped our negative control sequences, of which a single sequence bowtie 2 mapped to fex-1. our sample sequences mapped most closely […]

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

[…] laboratories. although 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. […]

PMCID: 4677295
PMID: 26658849
DOI: 10.1038/srep18081

[…] (). we next analyzed the five breast cancer rnaseq datasets (), sequenced to an average of 40 million sequencing reads per sample, using three different bioinformatic pipelines: rins, readscan and virusfinder 2.0. in no instance did we find any evidence of hpv, or other viral transcripts, in the samples that were positive for hpv dna., it is known that there are geographical variations […]


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VirusFinder institution(s)
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA
VirusFinder funding source(s)
Supported in part by National Institutes of Health grants (R01LM011177, P30CA68485, P50CA098131, and P50CA095103) and Ingram Professorship Funds.

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