Get familiar with the Sample page

Overview

The Sample page is your “home base” for operating within CZ GEN EPI. This page shows  all of the samples you and other members of your group have uploaded to CZ GEN EPI and includes important functions like search and filtering. The Sample page is also where you start the process for phylogenetic analyses using  Nextstrain and/or UShER.

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

About Your Samples

The Sample page provides general information about how many samples are currently uploaded and their privacy status.

Example Sample page highlighting number of uploaded samples and privacy status icons.

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).

View Metadata

The Sample page displays available metadata for each sample.

Example 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 it.
• Public ID: Refers to the GISAID ID. If a GISAID ID is not available, 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: SARS-CoV-2 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: Indicates whether or not a given sample has been submitted to the GISAID repository by the user, if it has been accepted (you will see an ISL Accession #) or rejected, or if the sample is not eligible for submission to the GISAID repository (private samples). This is an optional field.

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.

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.
• Genome Recovery: Select samples that have been completely (‘Complete’) or partially (‘Failed’) sequenced. This only applies to samples sequenced and uploaded by the Chan Zuckerberg Biohub.

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 Sample page showing how to select samples. Note that the number of samples you have selected displays above the right side of the samples table.

Example 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 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’.