VirusTAP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VirusTAP
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Tool usage distribution map

This map represents all the scientific publications referring to VirusTAP per scientific context
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Associated diseases

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Popular tool citations

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VirusTAP specifications

Information


Unique identifier OMICS_18178
Name VirusTAP
Alternative name Virus genome-Targeted Assembly Pipeline
Interface Web user interface
Input data Single- and PE NGS reads.
Output data Performs megablast and RAPSearch against virus nucleotide and protein databases.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Makoto Kuroda

Additional information


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Publication for Virus genome-Targeted Assembly Pipeline

VirusTAP citations

 (2)
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Identification of vaccine derived rotavirus strains in children with acute gastroenteritis in Japan, 2012 2015

2017
PLoS One
PMCID: 5597190
PMID: 28902863
DOI: 10.1371/journal.pone.0184067

[…] Reagent Kit v3 to generate 300-cycle paired-end reads. To construct contigs from the obtained short reads, de novo assembling were conducted using CLC genomics workbench (QIAGEN, Hilden, Germany) and VirusTap []. Contigs derived from either rotavirus wild-type strains or Rotarix strain were identified by BLAST search. Genotypes of each contigs were determined by an automated genotyping tool RotaC […]

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Whole genome analysis of human papillomavirus genotypes 52 and 58 isolated from Japanese women with cervical intraepithelial neoplasia and invasive cervical cancer

2017
PMCID: 5545048
PMID: 28785305
DOI: 10.1186/s13027-017-0155-4

[…] aries were analyzed on a MiSeq sequencer (Illumina) with the MiSeq reagent kit v3 (150¬†cycle). The complete genome sequences of HPV52/58 were de novo assembled from the total read sequences using the VirusTAP pipeline [] (https://gph.niid.go.jp/cgi-bin/virustap/index.cgi). The accuracy of the reconstructed whole-genome sequences was verified by read mapping with Burrows-Wheeler Aligner v0.7.12 [] […]


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VirusTAP institution(s)
Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
VirusTAP funding source(s)
Supported by a grant for Research on Emerging and Re-emerging Infectious Diseases (H25 Shinko-Ippan-015) from the Ministry of Health, Labour and Welfare, Japan, and the Research Program on Emerging and Re-emerging Infectious Diseases (15fk0108011h0003 and 15fm0108022h0001) from the Japan Agency for Medical Research and Development, AMED.

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