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In 2023, our team released a new pipeline for antimicrobial resistance (AMR) analysis. If you have been using the previous AMR module (referred to as the deprecated AMR module) you may be wondering if you can still use it to analyze data. The answer is YES. Note that the deprecated AMR pipeline will still run automatically on uploaded mNGS samples. Therefore, if interested, you will have a chance to compare results from both AMR modules. See Current vs Deprecated AMR Pipelines for information regarding differences between AMR pipelines. Here we list steps to view and download AMR detection results from the deprecated module, including heatmaps and reports.
Heatmap to Visualize AMR Detection across Samples
You can compare AMR detection across 2 or more metagenomic (mNGS) samples using heatmaps created with the deprecated AMR module. To do this:
1) Go to the Metagenomics tab within a Project page of interest and select two or more mNGS samples for analysis.
2) Click the heatmap icon and select "AMR Heatmap (Deprecated)"
3) The heatmap will open on a separate window. By default, the heatmap shows coverage for AMR genes on a logarithmic scale.
You can change the heatmap settings. The image shows the options within dropdown menus for View Level, Metric and Scale.
Download AMR Heatmap
To download the heatmap data in comma-delimited format, click on the Download button on the top right-hand side of the page and select “Download CSV”.
The downloaded heatmap file will include the following metrics:
Coverage: Percentage of the gene length where reads aligned.
Depth: Average read depth across the length of all alleles that were assigned a top scoring allele number.
Reads per million (rPM): Normalized number of reads that mapped to a given AMR gene.
Depth per million (dPM): Normalized depth
Mapped Reads: Total number of reads that mapped to a given AMR gene.
AMR Report Table
The AMR Report generated by the Deprecated AMR module summarizes AMR gene information and match quality metrics. This report is only available to users that have requested access to this feature.
To view the AMR Report Table:
1) Go to the Metagenomics tab listing mNGS samples and click on a sample of interest. This will take you to the Sample Report page, where you will see the "Antimicrobial Resistance (Deprecated)" tab. If you don’t see the tab, it means that you don’t have access to this feature.
2) Click the Antimicrobial Resistance (Deprecated) tab and explore the report. The report table specifies detected antibiotic classes, genes, coverage and depth.
View details regarding detected antibiotic classes by clicking on a class of interest.
Download Results from Deprecated AMR Module
All CZ ID users have access to AMR results generated through the deprecated AMR pipeline for samples uploaded through the mNGS pipeline. To download results from the deprecated AMR module:
1) Go to the Metagenomics tab listing mNGS samples and click on a sample of interest. This will take you to the Sample Report page. Click on the Download button on the top-right hand side of the page.
2) Select “View results folder” from the Download dropdown menu.
3) You will be directed to the Results Folder page. Navigate to the Srst2 results. Search the page for "Srst2" to find the results quickly (use shortcut keys Control+F or Command+F on PC or Mac devices, respectively).
There are two main output files, including:
Amr_summary_results.csv: This output file includes a summary of detected AMR genes, including gene family, total number of hits, coverage and depth.
Amr_processed_results.csv: This output file contains detailed information regarding the database version, reference AMR sequence information (genes, alleles, length, gene family) and sequence match metrics (e.g., divergence, coverage, depth).