Selected article for: "GenBank accession and negative control"
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_59
    Snippet: Reads unambiguously mapping to SARS-CoV or SARS-CoV-2 were aligned to the Wuhan-Hu-1 (Genbank accession MN908947.3) reference using bwa mem (Li, 2013). Variants were called using iVar, and pileups and consensus sequences were generated using samtools (Li et al., 2009; Grubaugh et al., 2019; Greenfield et al., 2020) . Any sample with more than 30,000 SARS-CoV-2 mapping reads and >99% coverage above 10x depth were taken as reliable samples, which r.....
    Document: Reads unambiguously mapping to SARS-CoV or SARS-CoV-2 were aligned to the Wuhan-Hu-1 (Genbank accession MN908947.3) reference using bwa mem (Li, 2013). Variants were called using iVar, and pileups and consensus sequences were generated using samtools (Li et al., 2009; Grubaugh et al., 2019; Greenfield et al., 2020) . Any sample with more than 30,000 SARS-CoV-2 mapping reads and >99% coverage above 10x depth were taken as reliable samples, which resulted in 95 samples (90 positive, 2 negative, 2 positive controls and 1 negative control). 92 clinical samples were compared to 4872 SARS-CoV-2 sequences from GISAID (as of April 10, 2020) (9, 10). All sequence filtering, alignments, phylogenetic inference, temporal ordering of sequences and geographic reconstruction of likely transmission events were done using nextstrain (Katoh and Standley, 2013; Sagulenko et al., 2018; Hadfield et al., 2018) .

    Search related documents:
    Co phrase search for related documents
    • bwa mem and Genbank accession: 1
    • clinical sample and consensus sequence: 1, 2
    • clinical sample and Genbank accession: 1, 2
    • clinical sample and negative control: 1, 2, 3, 4, 5, 6, 7, 8
    • clinical sample and positive control: 1, 2, 3, 4
    • clinical sample and reliable sample: 1
    • clinical sample and SARS mapping: 1
    • consensus sequence and Genbank accession: 1, 2, 3, 4, 5, 6, 7
    • consensus sequence and negative control: 1
    • consensus sequence and phylogenetic inference: 1, 2
    • Genbank accession and negative control: 1
    • Genbank accession and positive control: 1, 2
    • geographic reconstruction and phylogenetic inference: 1
    • geographic reconstruction and positive control: 1
    • GISAID SARS sequence and phylogenetic inference: 1
    • negative control and positive control: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • negative control and SARS mapping: 1
    • phylogenetic inference and positive control: 1
    • phylogenetic inference and SARS mapping: 1, 2