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CZ ID's AMR pipeline implements the Resistance Gene Identifier (RGI) tool for AMR sequence detection. The RGI tool is used to compare quality controlled reads and assembled contigs against AMR references sequences from the Comprehensive Antibiotic Resistance Database (CARD). Below is an overview of the AMR pipeline workflow.
All AMR pipeline versions implement RGI version 6 (v6.0.0). However, the AMR pipeline version will determine which version of CARD will be used to detect AMR genes. Samples uploaded to AMR pipeline v1.2.4 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.
See Upload or Select Data for AMR Analysis for details on how to run samples using the AMR pipeline. Note that there is an older AMR pipeline (known as the deprecated AMR pipeline) that implements a different workflow. See Current vs Deprecated AMR Pipelines to learn about differences between AMR pipelines. If you are interested in analyzing data with the older AMR workflow, you can still access results generated through the deprecated AMR pipeline (see Deprecated AMR Pipeline Results for details).
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