Data for validation STEC workflow

Additional data<br> ======== This archive contains additional data for the manuscript "Validation of a bioinformatics workflow for characterization of Shiga Toxin-Producing *Escherichia coli*, applied to a high-quality reference dataset, demonstrates high performance for using WGS for routine pathogen typing" # Notes Samples were analyzed with anonymized file names. They can be linked back to the original sample name as indicated in the Excel sheet. # Content ## Validation results ('all_results.xlsx') This spreadsheet contains detailed results for the validation. It contains all workflow output, corresponding metadata and classification (TP, FN, TN or FP). ## KMA output ('kma.tar') This folder contains the output from KMA for the various assays. They were executed in isolation for each of the assays (instead of with the workflow). <br> ## Example reports ('report_EH1236_*.zip') Example output reports of the workflow for each of the three detection methods on the same sample (EH1236). <br> ## Virulence gene custom database ('virulence_genes_db.fasta') This folder contains a FASTA file with the sequences that were used to evaluate the performance of the virulence gene detection. ## Virulence gene detection ('virulence_gene_detection.tar') This folder contains the output of the virulence gene detection for the three detection methods.<br> This was executed separately because the custom virulence gene database is not included in the bioinformatics workflow. ## Workflow reports ('workflow_reports_updated.tar') This folder contains the output of the workflow for all of the validation samples with the three detection methods. <br> All runs were executed in August 2020, with database updated to the latest available version. <br> A single archive is created for each sample, containing the output for the three bioinformatics approaches (BLAST+, KMA, SRST2).<br> BAM files were omitted from the archives due to their large sizes. ## Workflow reports - validation ('workflow_reports_validation.tar') This folder contains the output reports used for the validation (with older database version, etc).<br> This does not include KMA results because they were validated per-assay (see KMA archive). # Contact For further questions you can contact Bert Bogaerts ([e-mail])<br>