Selected article for: "bacterial fungal and positive test"
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_57
    Snippet: For the positive test, the same process was repeated using only SARS-CoV-2 genome (Supp Table 1 ). Positive results show >99% of SARS-CoV-2 reads uniquely map to either SARS-CoV or SARS-CoV-2, with the remaining 1% are ambiguous, potentially matching multiple taxa (Supp Table 2 ). All sequences were classified using the Kraken2 database. To remove the potential contamination of reads that are homologous across multiple species we used Kraken2 out.....
    Document: For the positive test, the same process was repeated using only SARS-CoV-2 genome (Supp Table 1 ). Positive results show >99% of SARS-CoV-2 reads uniquely map to either SARS-CoV or SARS-CoV-2, with the remaining 1% are ambiguous, potentially matching multiple taxa (Supp Table 2 ). All sequences were classified using the Kraken2 database. To remove the potential contamination of reads that are homologous across multiple species we used Kraken2 outputs to filter sequences to either human (uniquely matching Homo sapiens and no other taxon in our database), SARS-CoV-2 (either matching SARS-CoV or SARS-CoV-2 due to homology between these two viruses), and remaining reads that may be coming from unclassified, archaeal, bacterial, viral, fungal, protozoan or ambiguously mapping reads to human or SARS-CoV (Li, 2015).

    Search related documents:
    Co phrase search for related documents
    • positive result and potential contamination: 1, 2, 3, 4
    • positive result and SARS genome: 1, 2, 3, 4, 5, 6
    • positive result and virus homology: 1
    • positive test and potential contamination: 1
    • positive test and SARS genome: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20
    • potential contamination and SARS genome: 1
    • SARS genome and virus homology: 1