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># 补充数据 ======== 本归档文件对应论文《应用于高质量参考数据集的产志贺毒素大肠埃希菌（Shiga Toxin-Producing *Escherichia coli*）生物信息学分析流程验证：全基因组测序（Whole Genome Sequencing，WGS）用于常规病原分型展现优异性能》的补充数据。 ## 说明 所有样本均使用匿名文件名开展分析，可通过附带的Excel表格将匿名文件名与原始样本名进行关联。 ## 内容 ### 验证结果（`all_results.xlsx`） 该电子表格包含本次验证的详细结果，涵盖所有分析流程的输出结果、对应元数据以及分类标签（真阳性（TP）、假阴性（FN）、真阴性（TN）或假阳性（FP））。 ### KMA输出（`kma.tar`） 该文件夹包含针对各项检测单独运行KMA工具得到的输出结果（而非通过完整分析流程执行所得）。 ### 示例报告（`report_EH1236_*.zip`） 针对同一样本（EH1236），使用三种检测方法分别运行本分析流程得到的示例输出报告。 ### 毒力基因自定义数据库（`virulence_genes_db.fasta`） 该文件夹包含用于评估毒力基因检测性能的FASTA格式序列文件。 ### 毒力基因检测结果（`virulence_gene_detection.tar`） 该文件夹包含使用三种检测方法得到的毒力基因检测输出结果。由于本次分析使用的自定义毒力基因数据库未整合至本生物信息学流程中，因此该部分结果为单独运行所得。 ### 分析流程报告（`workflow_reports_updated.tar`） 该文件夹包含针对所有验证样本，使用三种检测方法运行本分析流程得到的输出结果。所有分析均于2020年8月执行，且数据库已更新至当时最新可用版本。 每个样本对应一个独立归档文件，其中包含三种生物信息学分析方法（BLAST+、KMA、SRST2）的输出结果。由于BAM文件体积过大，已从归档文件中移除。 ### 验证用分析流程报告（`workflow_reports_validation.tar`） 该文件夹包含用于本次验证的分析流程输出报告（使用旧版数据库等配置）。由于KMA结果已通过单项检测完成验证（详见KMA归档文件），因此该归档中不包含KMA结果。 ## 联系方式 如有进一步疑问，请联系Bert Bogaerts（邮箱：[e-mail]）