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.
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. Simply click a project name of interest listed under the Projects tab to navigate to its page.
- Project Name: Indicates you are viewing the project's page.
- Number of Samples: Indicates total number of samples uploaded to the project.
- Pipeline Tabs: Use tabs to view sample information and access reports for samples uploaded to each pipeline. Numbers the tabs indicate the number of samples ran through each pipeline.
- Sample Table: Summarizes sample metadata and metrics calculated through the pipeline run. Metrics and metadata columns displayed on the Sample Table will depend on the pipeline.
- Add Dropdown Menu: Use this menu to customize the table view by adding or removing columns.
The Project page contains similar features found in the Discovery page, such as Filter and Sample Information panels. Use the Filter panel on the left side of the page to find samples based on taxon information and metadata (click here for details). 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.
- Filter Icon: Summarizes number of applied filters. Click the icon to show or hide the filter panel.
- Filter Panel: Provides options to filter project samples based on specific taxa and/or metadata.
- Information Icon: Click the icon to show or hide the Information panel.
- Information Panel: Summarizes sample distribution within the project based on metadata. The following sections are 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 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.
- Share Button: Use this button to easily share the project with collaborators. You just need to provide their email and they will receive an invitation to access the project.
- Add Data Button: Click this button to upload samples to the project or edit metadata for existing samples.
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.
Steps to Download Data and Reports
- Select samples of interest.
- Click the Download icon to view file options and 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.
Steps to Delete Sample Runs
- Select samples of interest.
- Click the Trash icon and follow prompts to confirm 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.
- Toggle: Use toggle to see a sample list ( ), sample QC ( ), or a map ( ) showing the geographical distribution of samples
- Background Model Icon: Use this icon to create a background model.
- Heatmap Icon: Use this icon to create a heatmap.
- More Actions Dropdown Menu: Use this menu to create a phylogenetic tree or run the AMR pipeline.
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
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.
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 Add dropdown menu ("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/or Information panels located on either side of the page to gain space for the table. To hide the panels, simply click the Filter () and/or Information () icons.
- Filter Icon: Click the icon to hide or show the Filter panel.
- Information Icon: Click the icon to hide or show the Information panel.