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What is cAMRah?

In the field of bacterial genomics, identifying Antimicrobial Resistance Genes is a critical yet complex task. The current bioinformatic landscape is saturated with numerous software packages, each employing distinct algorithms, diverse reference databases, and non-standardized output formats. This heterogeneity often leads to conflicting results and complicates large-scale comparative analyses.

cAMRah (Combating Antibiotic-Resistant Bacteria in Africa - harmonized) is a curated, consensus-based workflow designed to address these challenges. Developed by researchers at J. Craig Venter Institute (JCVI), cAMRah integrates six established AMR-finder tools into a single, automated pipeline. Beyond simple execution, it harmonizes disparate outputs by mapping predictions to specific genomic loci and standardized ontologies.

Core Advantages

• Consensus-Based Detection: By leveraging tools such as AMRFinderPlus, ResFinder, RGI (CARD), and Abricate, cAMRah captures a more comprehensive representation of the resistome than any single tool could provide.
• Locus-Level Harmonization: A novel heuristic script groups multiple tool "hits" that fall within the same genetic coordinates. This prevents the overestimation of gene counts and clarifies which tools agree on a specific locus.
• Portability and Scalability: Utilizing Docker containers and Workflow Description Language (WDL), the pipeline ensures reproducible results across diverse computing environments, from local workstations to high-performance cloud platforms like Terra.bio.
• Ontology Standardization: All results are mapped to the Comprehensive Antibiotic Resistance Database (CARD) ontology, ensuring consistent gene naming conventions across all analyses.

Terra

Because cAMRah was built using WDL and containerized tools, it is well suited for the terra.bio platform. Terra is a collaborative project between the Broad Institute, Microsoft, and Verily. Terra.bio makes organizing your samples and analyses easy.

1. Selecting a workflow

Each containerized workflow is hosted on Dockstore. To find a workflow, go to the "WORKFLOWS" tab in your Terra.bio workspace. Then, select "Find a Workflow" and go to Dockstore.

On Dockstore, search for "JCVenterInstitute/CAMRA" to see all our available workflows. Once you have found the workflow you need, select Terra under the launch options.

2. Tool usage

Once a workflow is open in Terra, select the data you will analyze and define the input parameters. Some tasks, such as genome assembly, require a BV-BRC account username and password.

Past runs can be viewed under the "SUBMISSION HISTORY" tab and outputs can be found under "DATA"

Resources

Source code and additional documentation is available at GitHub.