Project Page

Jump to Section:

• Project Page Layout
• Sample Metrics and Metadata
• Customize Sample Table

In CZ ID, each sample you upload belongs to a project. Here we describe features within Project pages that will enable you to keep track of overall information regarding samples and pipeline run metrics within a given project.

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Project Page Layout

Once you select a project from the Discovery page, you will be directed to the project's page listing samples and project information. You can easily sort, filter, and search within your account to find projects of interest. 

Click on a project of interest to navigate to the project's page.

The Project page lists all the samples associated with the selected project and associated metrics. It also contains similar features found in the Discovery page, such as Filter and Sample Information panels. You can sort and filter the Sample Table to find samples of interest.

The Sample Information panel includes project description, overall sample numbers, date samples were uploaded to the project, and metadata. This will enable you to quickly visualize the distribution of samples within your project based on metadata.

Example project description and dropdown stats available through the Information panel.

Sections included in the Sample Information panel:

• Project description: Brief description (up to 700 characters) of the project provided during sample upload. You may edit the description at any time by clicking "Edit".
• Overall: Provides total number of samples, average number of reads per sample, and average number of reads passing host- and quality-filtering steps.
• Date created: Date samples were uploaded to the project.
• Metadata: Summarizes the distribution of samples within the project based on available metadata.

Share Project and Add or Edit Samples

You can share your project from the Project page by clicking the "Share" button on the upper right-hand side of the page. In addition, you can add samples to the project directly from the Project page or edit metadata for existing samples. To do this, click the "Add Data" button and follow prompts.

Download Sample Data and Reports

You can easily download data and reports for one or more samples from the Project page. To download, select samples you wish to download and click the Download icon on the right-hand side of the page. Follow prompts to select the file(s) you wish to download.

Delete Sample Runs

If you want to delete sample runs that you no longer need in your account (e.g., failed or test runs), you can use the Delete icon. Click here for details about sample run deletion.

Project Pages for Metagenomic Samples

Project pages for metagenomic samples include a toggle for you to see a sample list (default), sample QC, or a map showing the geographical distribution of samples. In addition, project pages for metagenomic samples include analysis icons for you to create background models, heatmaps, and phylogenetic trees, or run antimicrobial resistance (AMR) analysis using selected samples.

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Sample Table

The Sample Table displays a list of samples with associated metadata and metrics calculated through the pipeline run. You can sort the table to quickly identify samples of interest (e.g., high-quality samples), organize the sample list by metadata, or see the range of total reads across samples.

Sample Metrics and Metadata

The metrics and metadata columns displayed on the Sample Table will depend on the pipeline. Some columns will be included by default, but you can customize the table to add or remove columns. Below we describe the sample information provided in the Sample Table by pipeline and whether the information is shown by default. Table descriptions include metrics and metadata for mNGS Illumina and AMR, mNGS Nanopore, and Consensus Genome pipeline runs.

Sample Table for mNGS Illumina and AMR Pipeline Runs

Click here to see details about the mNGS pipeline for short-read data (Illumina). See Antimicrobial Resistance Workflow for an overview of the AMR pipeline.

Sample Table for mNGS Nanopore Pipeline Runs

Click here to see an overview of mNGS pipeline for long-read data (Nanopore).

Sample Table for Consensus Genome Pipeline Runs

Click here to learn about the Consensus Genome pipeline accessed through the mNGS Sample Report. See SARS-CoV-2 Pipeline to see details about the pipeline used for SARS-CoV-2 genome assembly. The Sample Table for consensus genomes includes genome metrics that are important to assess the quality of assembled consensus genomes.

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Customize Sample Table 

Columns included in the Sample Table will depend on the pipeline. The Samples Table defaults to a list of columns but you can add or remove columns by selecting the "plus" button in the right-hand corner of the table and selecting column names from the dropdown menu. 

If you are adding columns, you can remove the Filter and Information panels to gain space for the table. To hide the panels, simply click on the Filter and/or Sample Information icons.

Hide or show panels on either side of the Project page by clicking on the Filter and Sample Information icons.