VirusTAP protocols

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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 in pipelines

 (2)
2017
PMCID: 5545048
PMID: 28785305
DOI: 10.1186/s13027-017-0155-4

[…] 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 [] […]

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

[…] 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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VirusTAP in publications

 (3)
PMCID: 5597190
PMID: 28902863
DOI: 10.1371/journal.pone.0184067

[…] results of multiplex rt-pcr and stool culture. the viral titers of these viruses are also described in ., in sample no.1, 8,786 contigs were constructed by clc genomics workbench and 24 contigs by virustap. all the 11 genes of both rotavirus wild-type strain and rotarix strain were finally identified by blast search. shows the maps of short reads to cover each contig of vp6 gene, […]

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

[…] 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 [] […]

PMCID: 4988020
PMID: 27536332
DOI: 10.1186/s13027-016-0086-5

[…] purification of the dna library. next-generation sequencing was performed using a miseq reagent kit v3 (600-cycle; illumina, san diego, ca, usa). sequence reads were trimmed and assembled using the virustap pipeline software (https://gph.niid.go.jp/cgi-bin/virustap/index.cgi) []. sequence gap regions were amplified by conventional pcr, and sequenced using the sanger method. the complete genome […]


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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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