HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA | Zendy

Yuhan Hao | Zendy; Liying Yang | Zendy; Antonio Galvao Neto | Zendy; Milan R. Amin | Zendy; Dervla Kelly | Zendy; Stuart M. Brown | Zendy; Ryan C. Branski | Zendy; Zhiheng Pei | Zendy

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HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA

Author(s) -

Yuhan Hao,

Liying Yang,

Antonio Galvao Neto,

Milan R. Amin,

Dervla Kelly,

Stuart M. Brown,

Ryan C. Branski,

Zhiheng Pei

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty037

Subject(s) - metagenomics , contig , computational biology , shotgun , biology , false positive paradox , genotyping , shotgun sequencing , human papillomavirus , dna sequencing , genetics , papillomaviridae , dna , computer science , gene , genome , artificial intelligence , genotype , cervical cancer , medicine , cancer

Shotgun DNA sequencing provides sensitive detection of all 182 HPV types in tissue and body fluid. However, existing computational methods either produce false positives misidentifying HPV types due to shared sequences among HPV, human and prokaryotes, or produce false negative since they identify HPV by assembled contigs requiring large abundant of HPV reads.

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