Download QC metrics and mutation data

Overview

You can download quality control (QC) metrics and mutation data for sequences of interest in CZ GEN EPI. This data is obtained by automatically running sequences through Nextclade when uploading samples to the CZ GEN EPI platform. See Nextclade Quality Control and the “Data quality checks” section within Tree quality checks for details regarding QC metrics reported by Nextclade. Here we describe how to download QC metrics and mutation data for samples in your CZ GEN EPI account.

After reading this guide, you will:

• Learn how to download QC metrics and mutation data

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Downloading QC metrics and mutation data

To download a Nextclade report containing QC and mutation data in a tab-separated values file (".tsv"):

1. Select samples of interest from the table on the Sample page and click the "Download" icon.Click the "Download" icon on the right-hand side of the Sample page after selecting samples of interest.
2. Select “Sample Mutations and QC Metrics” within the Select Download dialog box. Note that you will see warnings if you select samples with no QC data available.Select "Sample Mutations and QC Metrics" from the "Select Download" dialog box. Once you make your selection, you can download it by clicking "Download".

If the selected samples lack QC data, a warning will appear. You will not be able to download the report.

3. Explore the downloaded file using Excel or a text editor of your choice for your surveillance work, which is discussed further here. The report file will contain all the QC metrics discussed here in tab-separated value format (".tsv").