Computational protocol: Viral Genome Sequencing Proves Nosocomial Transmission of Fatal Varicella

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Protocol publication

[…] Sequencing libraries were constructed as described elsewhere [, ] and sequenced on an Illumina MiSeq Sequencer. Data sets were trimmed and aligned against VZV strain Dumas (NC_001348.1) using BWA (version 0.7.12) [] and SAMTools software (version 1.0) []. Duplicate reads were removed, and a consensus sequence for each data set generated using in-house PERL scripts. Iterative repeat regions (R1, R2, R3, R4, and R5) and the terminal repeat region were excluded from analyses. OriS sequences were successfully captured within the read data and used to verify polymerase chain reaction–based results for all samples. Consensus sequences were aligned using MAFFT software (version 6) [], and a neighbor-joined phylogenetic tree, based on the Tamura-Nei model, was inferred using MEGA software (version 6.06) []. Genome sequences are available in GenBank (accession Nos. KP771912, KP771912, and 3 more awaiting assignment by GenBank as of 16 May 2016). […]

Pipeline specifications

Software tools BWA, SAMtools, MAFFT, MEGA
Application WGS analysis
Organisms Homo sapiens
Diseases Chickenpox, Encephalomyelitis, Acute Disseminated, Exanthema, HIV Infections