Data for validation STEC workflow

Additional data
========

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). 

## Example reports ('report_EH1236_*.zip')

Example output reports of the workflow for each of the three detection methods on the same sample (EH1236).

## 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.
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. 
All runs were executed in August 2020, with database updated to the latest available version. 
A single archive is created for each sample, containing the output for the three bioinformatics approaches (BLAST+, KMA, SRST2).
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).
This does not include KMA results because they were validated per-assay (see KMA archive).

# Contact

For further questions you can contact Bert Bogaerts (bert.bogaerts@sciensano.be)