PAIVS: prediction of avian influenza virus subtype |
Park, Hyeon-Chun
(Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea)
Shin, Juyoun (Department of Microbiology, College of Medicine, The Catholic University of Korea) Cho, Sung-Min (Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea) Kang, Shinseok (Chungbuk Veterinary Service Laboratory) Chung, Yeun-Jun (Department of Microbiology, College of Medicine, The Catholic University of Korea) Jung, Seung-Hyun (Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea) |
1 | Capua I, Alexander DJ. Avian influenza and human health. Acta Trop 2002;83:1-6. DOI |
2 | Tong S, Zhu X, Li Y, Shi M, Zhang J, Bourgeois M, et al. New world bats harbor diverse influenza A viruses. PLoS Pathog 2013;9:e1003657. DOI |
3 | Claes F, Morzaria SP, Donis RO. Emergence and dissemination of clade 2.3.4.4 H5Nx influenza viruses: how is the Asian HPAI H5 lineage maintained. Curr Opin Virol 2016;16:158-163. DOI |
4 | Pantin-Jackwood MJ, Costa-Hurtado M, Shepherd E, DeJesus E, Smith D, Spackman E, et al. Pathogenicity and transmission of H5 and H7 highly pathogenic Avian influenza viruses in mallards. J Virol 2016;90:9967-9982. DOI |
5 | Vemula SV, Zhao J, Liu J, Wang X, Biswas S, Hewlett I. Current approaches for diagnosis of influenza virus infections in humans. Viruses 2016;8:96. DOI |
6 | Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114-2120. DOI |
7 | Kim D, Langmead B, Salzberg S. HISAT2: graph-based alignment of next-generation sequencing reads to a population of genomes. Baltimore, MD: Johns Hopkins University, Center for Computational Biology, 2017. Accessed 2019 Dec 10. Available from: https://ccb.jhu.edu/software/hisat2/manual.shtml. |
8 | Danecek P, McCarthy SA. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics 2017;33:2037-2039. DOI |
9 | Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-1760. DOI |
10 | Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25:2078-2079. DOI |
11 | Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012;22:568-576. DOI |
12 | McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-1303. DOI |
13 | Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, et al. IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics 2015;31:2374-2376. DOI |
14 | Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics 2009;10:421. DOI |
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