paivs: prediction of avian influenza virus subtype

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ID: 138618
2020
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Abstract
Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype cause HPAI. Therefore, sensitive and accurate subtyping of AIV is important to prepare and prevent for the spread of HPAI. Next-generation sequencing (NGS) can analyze the full-length sequence information of entire AIV genome at once, so this technology is becoming a more common in detecting AIVs and predicting subtypes. However, an analysis pipeline of NGS-based AIV sequencing data, including AIV subtyping, has not yet been established. Here, in order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end users.
Reference Key
park2020genomicspaivs: Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Hyeon-Chun Park;Juyoun Shin;Sung-Min Cho;Shinseok Kang;Yeun-Jun Chung;Seung-Hyun Jung
Journal Journal of environmental management
Year 2020
DOI
10.5808/GI.2020.18.1.e5
URL
http://genominfo.org/upload/pdf/gi-2020-18-1-e5.pdf
Keywords
next-generation sequencing avian influenza virus

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