Download AMR Results & Data

Jump to Section:

• AMR Sample Report Page
• AMR Sequences
• Project Page

Overview

Here we describe how to download results and data generated through the AMR pipeline. You can download AMR results from AMR Sample Report or Project pages of interest. 

Learn about:

Files available for download through the Sample Report page

AMR Sample Report vs Comprehensive AMR Metric files

Files available for download through the Project page

Files included in the Antimicrobial Resistance Results download

---

Download Data from AMR Sample Report Page

You can download AMR result reports, sequence data, and intermediate files for a single sample from its AMR Sample Report page. Note that there are two reports containing AMR results, including the AMR Sample Report (or Report Table) and the Comprehensive AMR Metrics file (see report comparison below).

To download results from the AMR Sample Report page:

1) Navigate to the Antimicrobial Resistance tab within a Project page of interest. Click on a completed sample to view its AMR Sample Report page. 

2) Click the Download button on the right-hand side of the page and select the file of interest from the dropdown menu (see file descriptions below).

Download dropdown menu. Note that you can only download a Report Table with Applied Filters after applying filters (See Filtering AMR Sample Report).

Files available to download from the AMR Sample Report page

AMR Sample Report Table vs Comprehensive AMR Metrics

There are two reports available for download containing AMR results, namely the AMR Sample Report (or Report Table) and the Comprehensive AMR Metrics file. The AMR Sample Report contains the primary AMR detection results summarized through CZ ID, including AMR gene information, metrics for AMR reference sequence matches based on contig and read data, and pathogen-of-origin prediction results. See AMR Sample Report Metrics for details about information included in the report table.

The Comprehensive AMR Metrics file includes all the information provided within the AMR Sample Report in addition to intermediate file data, AMR metrics, and sequence information generated by the implemented Resistance Gene Identifier (RGI) tool. The Comprehensive AMR Metrics file will also specify whether a given contig match was nudged under a "Nudged_contig_amr" column (see Contig Metrics for information regarding nudged matches). In general, contig data within the Comprehensive AMR Metrics file is labeled “contig_amr” or “contig_sp”, whereas read data is labeled “kma_amr” or “kma_sp” reflecting the pipeline workflow (click here for details about the workflow). See table below describing equivalent terms between the AMR Sample Report and Comprehensive AMR Metrics files.

For details regarding metrics based on contigs and reads, see RGI main output details and Read mapping results at allele level, respectively.

---

Download AMR Sequence Data

To download read and/or contig sequences associated with an AMR gene, simply hover over the gene of interest and click the download icon.

You can choose between Reads and Contigs files for download (if available).

---

Download Data from Project Page

You can download reports for one or multiple samples from Project pages. Download files will be created and stored in your Downloads page. Files available through the Downloads page will be deleted after 7 days of creating the download. Note that the file options differ from those available for download through the AMR Sample Report page. 

To download AMR data from a Project page:

1) Go the Antimicrobial Resistance tab within the Project page of interest. Select sample(s) to download and click the Download icon on the right-hand side of the page.

2) A dialog box will appear where you can select the file of interest. Select the file and click "Start Generating Download" (see file description below).

Files available to download through the Project page 

The table below lists report and sequence data files available for download through the Project page. Most of the files will be downloaded as TAR.GZ compressed files. See How to Open a TAR.GZ File if you are not familiar with this format. Given that the Antimicrobial Resistance Results download option includes data associated with final reports, intermediate, and raw output files, we describe files found within this download.

Files Found within Antimicrobial Resistance Results Download

When you open the downloaded "Antimicrobial Resistance Results.tar.gz" file, you will see three folders per selected sample. These folders contain final report, intermediate, and raw output files. Note that non-host read and contig sequences (FASTA) will also be available through this download for pipeline versions prior to AMR Pipeline v1.1.