Table 1 Overview of data files/data sets
Label | Name of data file/data set | File types (file extension) | Data repository and identifier (DOI or Accession Number) | License |
|---|---|---|---|---|
OSCAR protocol (methods) | File name: OSCAR protocol Details: This contains the full laboratory and bioinformatics methods Data set: Oxford Screening of CSF and Respiratory Samples (‘OSCAR’): Supplementary resources for a project using next generation sequencing (NGS) for identification of viruses from clinical laboratory samples | Portable document format (.pdf) | Figshare https://dx.doi.org/10.6084/m9.figshare.5670007 (Data citation 1) | CC-BY 4.0 |
Benefits and challenges of meta-genomic sequencing | File name: OSCAR table benefits and challenges Details: This table summarises some of the benefits and challenges associated with the application of metagenomic approaches (next generation sequencing, NGS) to the clinical diagnosis of viral infection Data set: Oxford Screening of CSF and Respiratory Samples (‘OSCAR’): Supplementary resources for a project using next generation sequencing (NGS) for identification of viruses from clinical laboratory samples | Portable document format (.pdf) | Figshare https://dx.doi.org/10.6084/m9.figshare.5670007 (Data citation 1) | CC-BY 4.0 |
Metadata for 20 samples used for meta-genomic sequencing | File name: OSCAR 20 samples metadata Details: This table contains the anonymised demographic and clinical details of 20 clinical samples (10 respiratory and 10 CSF), from a UK hospital microbiology laboratory, which were processed using a metagenomic pipeline Data set: Oxford Screening of CSF and Respiratory Samples (‘OSCAR’): Supplementary resources for a project using next generation sequencing (NGS) for identification of viruses from clinical laboratory samples | This file is available in Microsoft excel (.xlsx) and as comma separated variables (.csv) | Figshare https://dx.doi.org/10.6084/m9.figshare.5670007 (Data citation 1) | CC-BY 4.0 |
Krona plots of meta-genomic data | Oxford Screening of CSF and Respiratory Samples (‘OSCAR’): interactive data visualisation using Krona to display results from a pilot project using next generation sequencing (NGS) for identification of viruses from clinical laboratory samples | Hypertext Markup Language (.html) | Figshare https://dx.doi.org/10.6084/m9.figshare.5712091 (Data citation 2) | CC-BY 4.0 |
Sequence data | HHV6 reads and metagenomic data from clinical samples | Metagenomic sequences: Fastq HHV-6 reads are available in BAM and Fastq format | European Molecular Biology Laboratory (EMBL); European Nucleotide Archive (primary Accession PRJEB22949) (Data citation 3). Individual accession numbers (Data citations 4–27): SAMEA104355484; SAMEA104355485; SAMEA104355486 ; SAMEA104355487; SAMEA104421606; SAMEA104421607; SAMEA104421608; SAMEA104421609; SAMEA104421610; SAMEA104421611; SAMEA104355484; SAMEA104421613; SAMEA104421614; SAMEA104421615; SAMEA104421616; SAMEA104421617 ; SAMEA104421618; SAMEA104421619; SAMEA104421620; SAMEA104421621; SAMEA104355485; SAMEA104355486; SAMEA104355487; SAMEA104421625 | Open access in accordance with ENA policy (https://www.ebi.ac.uk/ena/standards-and-policies) |