VirusSeeker specifications


Unique identifier OMICS_15195
Name VirusSeeker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 0.03
Stability Stable
Newbler, Phrap
Maintained Yes


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  • person_outline Guoyan Zhao <>

Publication for VirusSeeker

VirusSeeker in publications

PMCID: 5946436
PMID: 29751830
DOI: 10.1186/s40168-018-0475-7

[…] using a 2100 bioanalyzer (agilent technologies). multiplexed sia libraries were pooled and sequenced separately from multiplexed mda libraries., illumina sequencing reads were analyzed using virusseeker [], a blast-based computational pipeline to identify viral sequences. taxonomic classification for bacteriophage sequences were parsed using megan version 6.10.2 []. ecological analyses […]

PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] by pathseq (kostic et al., ), surpi (naccache et al., ), clinical pathoscope (byrd et al., ), exhaustive iterative assembly (schürch et al., ), vip (li et al., ), taxonomer (flygare et al., ), and virusseeker (zhao et al., ). pathseq removes human reads in a series of filtering steps in an attempt to concentrate pathogen-derived data. clinical pathoscope filters human genomic reads as well […]

PMCID: 5532837
PMID: 28751399
DOI: 10.1128/genomeA.00698-17

[…] blood specimen collected from a free-living lemur (indri indri) in the betampona nature reserve, toamasina province, madagascar (s17.931389 and e49.20333). bioinformatic analyses performed using the virusseeker computational pipeline () identified illumina sequencing reads with limited identity to known anelloviruses. the resulting complete genome was amplified in overlapping pcr fragments using […]

PMCID: 5490804
PMID: 28538703
DOI: 10.3390/v9060127

[…] has recently been reviewed [,]. moreover, new tools are continually emerging, such as virsorter [] and metaphinder [], both designed for the detection of viral sequences in metagenomic data; virusseeker, released in early 2017 (mainly focused on eukaryotic viruses, though it does incorporate bacteriophage analysis in the pipeline []); and the ivirus community resource, which provides […]

PMCID: 4770319
PMID: 26924426
DOI: 10.1038/srep22361

[…] products were pooled for sequencing on the illumina miseq platform (illumina, san diego. ca). metagenomic profiling of the shotgun datasets was carried out using the customized informatics pipeline virusseeker to computationally identify viral sequences. the study protocol was approved by the ethics committee of the china cdc, and was performed according to chinese ethics laws and regulations. […]

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VirusSeeker institution(s)
Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
VirusSeeker funding source(s)
This work was supported in part by NIH grant U54 AI057160 to the Midwest Regional Center of Excellence for Biodefense and Emerging Infectious Disease Research, NIH grant U19AI109725-03 and K99 DK107923.

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