Data for validation STEC workflow

<p>Additional data<br> ========</p> <p>This archive contains additional data for the manuscript &quot;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&quot;</p> <p># Notes</p> <p>Samples were analyzed with anonymized file names. They can be linked back to the original sample name as indicated in the Excel sheet.</p> <p># Content</p> <p>## Validation results (&#39;all_results.xlsx&#39;)</p> <p>This spreadsheet contains detailed results for the validation. It contains all workflow output, corresponding metadata and classification (TP, FN, TN or FP).</p> <p>## KMA output (&#39;kma.tar&#39;)</p> <p>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).&nbsp;</p> <p><br> ## Example reports (&#39;report_EH1236_*.zip&#39;)</p> <p>Example output reports of the workflow for each of the three detection methods on the same sample (EH1236).</p> <p><br> ## Virulence gene custom database (&#39;virulence_genes_db.fasta&#39;)</p> <p>This folder contains a FASTA file with the sequences that were used to evaluate the performance of the virulence gene detection.</p> <p>## Virulence gene detection (&#39;virulence_gene_detection.tar&#39;)</p> <p>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.</p> <p>## Workflow reports (&#39;workflow_reports_updated.tar&#39;)</p> <p>This folder contains the output of the workflow for all of the validation samples with the three detection methods.&nbsp;<br> All runs were executed in August 2020, with database updated to the latest available version.&nbsp;<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.</p> <p>## Workflow reports - validation (&#39;workflow_reports_validation.tar&#39;)</p> <p>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).</p> <p># Contact</p> <p>For further questions you can contact Bert Bogaerts (bert.bogaerts@sciensano.be)<br> &nbsp;</p>