Upload or Select Data for AMR Analysis

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• Upload Data
• Select mNGS Samples

Overview

Here we describe how to kick off your antimicrobial resistance (AMR) analysis within CZ ID. There are two options for submitting data for AMR analysis. You can upload a new dataset to your CZ ID account or you can select metagenomic (mNGS) samples already on your account.

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Upload Data for AMR Analysis

To upload data for AMR analysis:

1) Log in to your CZ ID account.

2) Navigate to the Upload page from your Discovery page. Note that the upload process is divided into three general sections, including Samples, Metadata, and Review sections.

3) Select or create a project, select analysis type, and upload files on the Sample Upload page. Note that you can run AMR and metagenomic (mNGS) analyses at the same time on uploaded samples. 

a) Selecting or creating a project

You can choose to upload samples to an existing project or create a new one. The project will affect the pipeline version used to run the samples (see Pipeline Version below). To create a new project, fill out the appropriate information on the New Project dialog box that will appear after clicking on "Create Project".

b) Selecting analysis type

For the analysis type you can select "Antimicrobial Resistance" alone or choose to run metagenomic analysis (mNGS) at the same time. Note that the AMR pipeline is only available for short-read data (Illumina).

Pipeline Version

The pipeline version that will be used to run uploaded samples is specified within your choice of analysis type. Important pipeline versioning information:

• The AMR pipeline version will dictate which version of the Comprehensive Antibiotic Resistance Database (CARD) will be used to detect AMR genes. Samples uploaded to AMR pipeline v1.2.4 and later will be compared against CARD v3.2.6, whereas samples uploaded to prior versions will use CARD v3.2.3. The latest CARD (v3.2.6) contains 122 additional AMR genes compared to database v3.2.3.
• Metagenomic samples uploaded to projects created after April 19, 2023 (mNGS pipeline v8.0 and up) will run on the latest pipeline available with updated QC and host filtering steps (click here for details). Given that the AMR pipeline uses the same host filtering as the mNGS pipeline, this also applies to AMR samples. AMR samples uploaded to projects created after April 19, 2023 will run with updated QC and host filtering steps.
• Metagenomic samples selected for AMR analysis (see section below):
  • Samples run on mNGS pipeline v8.0 (and later) that are selected for AMR analysis will be compared against the latest CARD (v3.2.6).
  • Samples run on pipeline versions prior to mNGS pipeline v8.0 that are selected for AMR analysis will be compared against CARD v3.2.3.

c) Uploading sequence file(s)

You can upload sample files from your computer or through your BaseSpace account. For details, see Selecting Files.

4) Continue to the next section, Upload Metadata.

5) Fill out the appropriate metadata. Note that there are six required metadata fields, including: Host Organism, Sample Type, Water Control, Nucleotide Type, Collection Date, and Collection Location. See Adding Metadata for details.

You can enter required metadata manually or upload a metadata file in comma-delimited format (“csv” file extension). See Adding Metadata for details.

6) Continue to the next section, Review.

7) Review the project, sample, and analysis information. Use "edit" links by each review category to edit information as needed. Accept the CZ ID terms of service and click “Start Upload”.

Start upload after reviewing submission information and accepting the CZ ID terms of service.

You will see a popup indicating the status of your sample upload. Once upload is completed, go to the project page to view the status of your samples.

8) Go to the Project page to view the status of your samples. Click on the Antimicrobial Resistance tab to check on the AMR analysis status. See Sample Table for details about metadata and metrics calculated through the pipeline run. 

Project page showing uploaded samples for AMR analysis. The number of AMR samples and their status can be found under the “Antimicrobial Resistance” tab. 

9) Once the AMR pipeline run is completed, you can view the AMR Sample Report and download results.

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Select mNGS Samples for AMR Analysis

You can perform AMR analyses on samples that have already run through the short read (Illumina) mNGS pipeline. This feature is only available for mNGS samples run on Illumina mNGS pipeline v5.0 and later.

To select mNGS samples from your account:

1) Go to the Project page of interest and and select the mNGS sample(s) for AMR analysis. Click on the More Actions icon and select "Runa Antimicrobial Resistance Pipeline" to start AMR analysis on selected samples.

Select samples and click the More Actions icon. Select "Run Antibiotic Resistance Pipeline" to begin the analysis.

2) You will see a confirmation or warning message on the top right-hand corner of the page.

If everything is working well, you will see a popup message highlighted in blue indicating that samples are running on the Antimicrobial Resistance pipeline.

You will see a popup message highlighted in yellow if the AMR analysis failed to launch. Make sure you are not trying to run samples that have been already submitted for AMR analysis.

3) Go to the Antimicrobial Resistance tab to check on the analysis status.

Project page showing mNGS samples used for AMR analysis. The number of AMR samples and their status can be found under the “Antimicrobial Resistance” tab. 

4) Once the AMR pipeline run is completed, you can view the AMR Sample Report and download results.