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VirusSeq specifications


Unique identifier OMICS_00227
Name VirusSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for VirusSeq

VirusSeq citations


Overview of Virus Metagenomic Classification Methods and Their Biological Applications

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

[…] rins, slim, surpi, taxy-pro, “unknown pathogens from mixed clinical samples,” vip and viromescan), or even days (5 workflows: exhaustive iterative assembly, viralfusionseq, virfind, virusfinder and virusseq)., for 17 workflows for which these data were available, we looked for correlations by plotting performance scores against the analysis steps included (figure ). workflows that included […]


Current Bioinformatics resources in combating infectious diseases

PMCID: 5818640
PMID: 29497257
DOI: 10.6026/97320630014031

[…] two hours [, ]. the rins is an intersection-based pathogen detection workflow that utilizes a user-reference genome set for the identification of non-human sequences in deep sequencing datasets. virusseq is an algorithmic method that is also used for detecting known viruses and their integration sites in the human genome using ngs data. virusseq was developed using perl platform […]


A pilot systematic genomic comparison of recurrence risks of hepatitis B virus associated hepatocellular carcinoma with low and high degree liver fibrosis

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

[…] virus-induced host genome instability and viral genome variability [, ]. it has been shown that virusfinder performs better than other state-of-the-art virus integration detection pipelines such as virusseq [] and virusfusionseq [] in terms of both accuracy and time efficiency []. our virus integration detection pipeline was based on virusfinder, with several modifications. firstly, […]


Genomic characterization of human papillomavirus positive and negative human squamous cell cancer cell lines

PMCID: 5689691
PMID: 29156801
DOI: 10.18632/oncotarget.21174

[…] we described previously [, ]. we stained the rppa slides with 305 unique antibodies (), which were analyzed as we previously described []., for hpv detection and integration analysis, we applied the virusseq pipeline previously developed in the department of bioinformatics and computational biology at the university of texas md anderson cancer center []. the hpv detection analysis began […]


Analysis of the whole transcriptome from gingivo buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy

PLoS One
PMCID: 5590820
PMID: 28886030
DOI: 10.1371/journal.pone.0183606

[…] included in the study (table a in ). choice of adjacent control tissue from same patient was intentional to minimize inter-individual differences in tobacco exposure and the affected tissue site., virusseq algorithm[], which uses subtraction method to detect viruses and integration sites, was applied to identify patients with or without infection of any virus such as hbv, hcv, hiv including […]


Cross species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates

Nat Commun
PMCID: 5013636
PMID: 27574101
DOI: 10.1038/ncomms12601

[…] mrnas and mirnas, and detection of enriched transcription factor targets, we used a cutoff of q-value<0.25 and fold-change exceeding 1.25 × ., viral and fusion transcripts were assessed using the virusseq algorithm given that mapping viral integration sites is computationally similar to identifying fusion events. in brief, non-human reads were aligned to viral sequences from the genome […]

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VirusSeq institution(s)
Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

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