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1
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nasopharyngeal/oropharyngeal (NP/OP) swabs
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Sample collection from hospitalized paediatric patients and household cohort for viral diagnostics
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34997042
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View Related Publication
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2
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multiplex real-time PCR
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Screening samples for 15 respiratory virus targets
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3
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Light Diagnostic RSV DFA kit (Chemicon, Millipore Corporation, USA)
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Detection of RSV antigen using a direct ImmunoFluorescent Antibody Test (IFAT)
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4
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DNase
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Removal of free non-encapsidated DNA from samples during total nucleic acid extraction
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5
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reverse transcription with non-ribosomal random hexamers
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Conversion of RNA to DNA, avoiding rRNA targets, for sequencing preparation
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6
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Illumina HiSeq 2500
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Generating 2–3 million 250 nt paired-end reads/sample for sequencing
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7
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MAFFT
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Aligning viral contigs and genomes for sequence analysis
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8
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RAxML
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Constructing maximum-likelihood phylogenetic trees for virus genome comparison
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9
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SPAdes v.3.10
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De novo assembly of quality controlled reads from sequencing
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10
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UBLAST
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Identifying viral contigs using virus family protein databases
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11
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AliView
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Manual checking of aligned sequences
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12
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FigTree v.1.4.3
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Visualizing phylogenetic trees
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