Get familiar with Sample page

Overview

CZ GEN EPI supports genomic epidemiology analysis of viral pathogens. Each pathogen workspace has a Sample page where can see all of the samples you and members of your group have uploaded to CZ GEN EPI. The Sample page is your “home base” for operating within CZ GEN EPI, where you upload samples and launch phylogenetic analyses using  Nextstrain and/or UShER.  This page also includes important functions like search and filtering.

After reading this user guide, you will be able to:

• Navigate around the the Sample page
• Use all of the functionality available on the Sample page

Upload Samples

Upload samples for a given pathogen through the Sample page.

Easily upload samples from the Sample page

Keep Track of Samples

The Sample page provides general information about how many samples are currently uploaded in given pathogen workspace, their privacy status, and quality.

Example SARS-CoV-2 Sample page highlighting number of uploaded samples, privacy status icons and quality.

You can quickly glance the following information from your Sample page:

• Total number of samples: The number of samples in your group is listed at the top of the Samples tab on the top left side of the screen.
• Public vs private samples: Public samples will have a globe icon, whereas samples that have been set to Private will have a lock icon. Private samples are not visible to groups with which you have a data sharing agreement (e.g. CDPH with California local health jurisdictions).
• Quality: The quality of each sample is automatically assessed based on total quality scores determined by Nextclade. Sample QC tags may indicate "good" (green), "mediocre" (yellow), or "bad" (red) based on quality score thresholds. 

View Metadata

The Sample page displays available metadata for each sample.

Example SARS-CoV-2 Sample page highlighting metadata column headers.

The metadata includes:

• Private ID: Identifier that you specify for each sample at the time of sample upload. Only users in your Group can see this ID.
• Public ID: Refers to the SARS-CoV-2 isolate name from a public repository (GenBank or GISAID ID) or to the GenBank accession ID for Mpox. If an isolate name (SARS-CoV-2) or accession ID (Mpox) is not provided, the CZ GEN EPI platform will automatically generate a Public ID based on when the sample was uploaded (sequential number/year). Note that private samples will also receive a Public ID. However, private samples will not be visible to other groups.
• Collection Date: User-provided date on which the sample was collected from an individual or an environment.
• Lineage: Virus lineage for each sample will be automatically detected and assigned by the platform after a few minutes. Lineages are assigned using the UShER phylogenetic placement tool. Lineage phylogenetic placement is verified routinely and updated as needed. Therefore, lineage assignments might change over time in your dashboard.
• Upload Date: Date that the sample was uploaded to CZ GEN EPI.
• Collection Location: User-provided geographic location where the sample was collected (at the county level or above). Follows the format: Region/Country/Division/Location
• Sequencing Date: User-provided date on which the sample was sequenced. This is an optional field.
• GISAID (see note): Indicates whether or not a sample has been submitted to the GISAID repository by the user. This column is only included in the SARS-CoV-2 workspace. If the sample has been submitted and accepted by GISAID, you will see a GISAID ID (e.g., hCoV-19/USA/IA-SHL-2264571/2023) for the Public ID. If the sample was not accepted, you will see "Not accepted" under the GISAID column. If the sample is private or has not been submitted to GISAID,  it will read "Not found". This is an optional field. 

Note on GISAID

As of April 13, 2023 CZ GEN EPI is only using GenBank to automatically collect SARS-CoV-2 contextual samples for phylogenetic analyses instead of GISAID. You may notice that the GISAID column is no longer available on the metadata table. Click here to learn more details about the transition from GISAID to GenBank.

Filter & Search Samples

You can filter the samples that appear in your sample list to easily search for samples of interest. You can also search directly for specific samples using the search box above the sample table. The search will try to match entries on any of the metadata fields.

SARS-CoV-2 Example Sample page highlighting filter menu and search box. 

The available filters include:

• Upload Date: Select samples uploaded during a specific  date range or  within preset intervals( Today, Yesterday, or Last 7 Days).
• Collection Date: Select samples collected during a specific date range or those collected within preset intervals (Last 7 Days, Last 30 Days, Last 3 Months, Last 6 Months, or Last Year).
• Lineage: Select samples representing specific lineages. You may select one or more lineages from the list.
• QC status: You can specify if you only want to see samples with "Good" quality. 

Select Samples

You can select samples for downstream analyses by checking the boxes to the left of the samples. You can select all the samples showing on your sample table or select specific samples. 

Example SARS-CoV-2 Sample page showing how to select samples. Note that the number of samples you have selected displays above the right-hand side of the samples table.

Example SARS-CoV-2 Sample page showing how to select all samples on your sample table.

Run Phylogenetic Analysis & Manage Data

After selecting samples of interest, you can run phylogenetic analyses and/or manage your data (edit, download, and/or delete samples). 

Example SARS-CoV-2 Sample page highlighting icons for the following dropdown menus: Running Phylogenetic Analysis, Download, and More Actions.

• To run phylogenetic analysis and/or manage data on selected samples, see the following dropdown menus:three actions available (from left to right) are:
• Run Phylogenetic Analysis: Select from Nextstrain Phylogenetic Tree or UShER Phylogenetic Analysis.
• Download:Select the type of data you would like to download, including  Consensus Genome (.fasta) and/or Sample Metadata (.tsv).
• More Actions: Select to Edit Samples or Delete Samples.