Selected article for: "phylogenetic tree and SARS genome"
Author: Daniel J Butler; Christopher Mozsary; Cem Meydan; David C Danko; Jonathan Foox; Joel Rosiene; Alon Shaiber; Ebrahim Afshinnekoo; Matthew MacKay; Fritz J Sedlazeck; Nikolay A Ivanov; Maria A Sierra; Diana Pohle; Michael Zeitz; Vijendra Ramlall; Undina Gisladottir; Craig D Westover; Krista Ryon; Benjamin Young; Chandrima Bhattacharya; Phyllis Ruggiero; Bradley W Langhorst; Nathan A Tanner; Justyn Gawrys; Dmitry Meleshko; Dong Xu; Jenny Xiang; Angelika Iftner; Daniela Bezdan; John Sipley; Lin Cong; Arryn Craney; Priya Velu; Ari Melnick; Iman A Hajirasouliha; Thomas Iftner; Mirella Salvatore; Massimo Loda; Lars F Westblade; Shawn Levy; Melissa Cushing; Nicholas P Tatonetti; Marcin Imielinski; Hanna Rennert; Christopher Mason
Title: Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
  • Document date: 2020_4_20
    • ID: kyoa5gsf_17
    Snippet: We then investigated clinical samples with sufficient coverage across the 30kb SARS-CoV-2 genome (>10x) to identify genetic variants and place NYC strains onto phylogenetic tree of the global outbreak. We identified variants both through alignment and de novo assembly of Krakenclassified SARS-CoV-2 reads. In both cases, single nucleotide variants (SNVs) and indels (insertions/deletions) were called relative to the SARS-CoV-2 reference sequence (G.....
    Document: We then investigated clinical samples with sufficient coverage across the 30kb SARS-CoV-2 genome (>10x) to identify genetic variants and place NYC strains onto phylogenetic tree of the global outbreak. We identified variants both through alignment and de novo assembly of Krakenclassified SARS-CoV-2 reads. In both cases, single nucleotide variants (SNVs) and indels (insertions/deletions) were called relative to the SARS-CoV-2 reference sequence (GCF_009858895.2) and then compared with 4,964 sequenced samples in GISAID (downloaded on 4/12/2020) using the Nextstrain database (Hadfield et al., 2018) .

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