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Table 1 Overview of data files/data sets

From: Oxford Screening CSF and Respiratory samples (‘OSCAR’): results of a pilot study to screen clinical samples from a diagnostic microbiology laboratory for viruses using Illumina next generation sequencing

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://0-dx-doi-org.brum.beds.ac.uk/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://0-dx-doi-org.brum.beds.ac.uk/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://0-dx-doi-org.brum.beds.ac.uk/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://0-dx-doi-org.brum.beds.ac.uk/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)