NCBI-AMRFinderPlus¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
| Standalone | Bacteria, Mycotics | PHB v2.2.0 | Yes | Sample-level |
NCBIAMRFinderPlus_PHB¶
AMRFinderPlus identifies acquired antimicrobial resistance (AMR) genes, virulence genes, and stress genes. Such AMR genes confer resistance to antibiotics, metals, biocides, heat, or acid. For some taxa (see here), AMRFinderPlus will provide taxa-specific results including filtering out genes that are almost ubiquitous in the taxa (intrinsic genes) and identifying resistance-associated point mutations. In TheiaProk, the taxon used by AMRFinderPlus is specified based on the gambit_predicted_taxon or a user-provided expected_taxon.
You can check if a gene or point mutation is in the AMRFinderPlus database here, find the sequences of reference genes here, and search the query Hidden Markov Models (HMMs) used by AMRFinderPlus to identify AMR genes and some stress and virulence proteins (here). The AMRFinderPlus database is updated frequently. You can ensure you are using the most up-to-date version by specifying the docker image as a workflow input. You might like to save this docker image as a workspace data element to make this easier.
📋 Use Cases¶
- To run ONLY AMRFinderPlus software instead of running the entire TheiaProk workflow. This workflow will run much faster than the TheiaProk workflows.
- To update AMRFinderPlus results when a new version of the software and/or its database are released by the NCBI developers.
Inputs¶
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| amrfinderplus_wf | assembly | File | Genome assembly file in FASTA format. Can be generated by TheiaProk workflow or other bioinformatics workflows. | Required | |
| amrfinderplus_wf | samplename | String | Name of the sample to be analyzed | Required | |
| amrfinderplus_nuc | cpu | Int | Number of CPUs to allocate to the task | 8 | Optional |
| amrfinderplus_nuc | detailed_drug_class | Boolean | False | Optional | |
| amrfinderplus_nuc | disk_size | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
| amrfinderplus_nuc | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:3.11.20-2023-09-26.1" | Optional |
| amrfinderplus_nuc | hide_point_mutations | Boolean | If set to true, the output File amrfinderplus_all_report will not include any POINT mutations identified by AMRFinderPlus. | False | Optional |
| amrfinderplus_nuc | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 16 | Optional |
| amrfinderplus_nuc | mincov | Float | "Minimum proportion of reference gene covered for a BLAST-based hit (Methods BLAST or PARTIAL)." Attribute should be a float ranging from 0-1, such as 0.6 (equal to 60% coverage) | 0.5 | Optional |
| amrfinderplus_nuc | minid | Float | "Minimum identity for a blast-based hit hit (Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs." Attribute should be a float ranging from 0-1, such as 0.95 (equal to 95% identity) | 0.90 | Optional |
| amrfinderplus_nuc | organism | String | If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica" | Optional | |
| version_capture | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | timezone | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | Optional |
Outputs¶
| Variable | Type | Description |
|---|---|---|
| amrfinderplus_all_report | File | Output TSV file from AMRFinderPlus (described here) |
| amrfinderplus_amr_classes | String | AMRFinderPlus predictions for classes of drugs that genes found in the reads are known to confer resistance to |
| amrfinderplus_amr_core_genes | String | AMR genes identified by AMRFinderPlus where the scope is "core" |
| amrfinderplus_amr_plus_genes | String | AMR genes identified by AMRFinderPlus where the scope is "plus" |
| amrfinderplus_amr_report | File | TSV file detailing AMR genes only, from the amrfinderplus_all_report |
| amrfinderplus_amr_subclasses | String | More specificity about the drugs that genes identified in the reads confer resistance to |
| amrfinderplus_db_version | String | AMRFinderPlus database version used |
| amrfinderplus_stress_genes | String | Stress genes identified by AMRFinderPlus |
| amrfinderplus_stress_report | File | TSV file detailing stress genes only, from the amrfinderplus_all_report |
| amrfinderplus_version | String | AMRFinderPlus software version used |
| amrfinderplus_virulence_genes | String | Virulence genes identified by AMRFinderPlus |
| amrfinderplus_virulence_report | File | TSV file detailing virulence genes only, from the amrfinderplus_all_report |
| amrfinderplus_wf_analysis_date | String | Date of analysis |
| amrfinderplus_wf_version | String | Version of PHB used for the analysis |
References¶
Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021 Jun 16;11(1):12728. doi: 10.1038/s41598-021-91456-0. PMID: 34135355; PMCID: PMC8208984. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8208984/