AMR Search¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level | Dockstore |
|---|---|---|---|---|---|
| Standalone | Any taxa | v3.0.1 | Yes | Sample-level | AMR_Search_PHB |
AMR_Search_PHB¶
AMR_Search Workflow Diagram
The AMR_Search workflow is a standalone version of Pathogenwatch's AMR profiling functionality utilizing AMRsearch tool from Pathogenwatch.
A limited number of species are currently supported and are listed below. NCBI codes are needed from this table to select the correct library.
| Species | NCBI Code |
|---|---|
| Neisseria gonorrhoeae | 485 |
| Staphylococcus aureus | 1280 |
| Salmonella typhi | 90370 |
| Streptococcus pneumoniae | 1313 |
| Klebisiella | 570 |
| Klebsiella pneumoniae | 573 |
| Candida auris | 498019 |
| Vibrio cholerae | 666 |
| Campylobacter | 194 |
Inputs¶
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| amr_search_workflow | amr_search_database | String | NCBI taxon code of samples known taxonomy, see above supported species | Required | |
| amr_search_workflow | input_fasta | File | A microbial assembly file | Required | |
| amr_search_workflow | samplename | String | The name of the sample being analyzed | Required | |
| amr_search | cpu | Int | Number of CPUs to allocate to the task | 2 | Optional |
| amr_search | disk_size | Int | Amount of storage (in GB) to allocate to the task | 50 | Optional |
| amr_search | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1 | Optional |
| amr_search | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | 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 |
Workflow Tasks¶
amr_search: Antimicrobial resistance profiling
This task performs in silico antimicrobial resistance (AMR) profiling for supported species using AMRsearch, the primary tool used by Pathogenwatch to genotype and infer antimicrobial resistance (AMR) phenotypes from assembled microbial genomes.
AMRsearch screens against Pathogenwatch's library of curated genotypes and inferred phenotypes, developed in collaboration with community experts. Resistance phenotypes are determined based on both resistance genes and mutations, and the system accounts for interactions between multiple SNPs, genes, and suppressors. Predictions follow S/I/R classification (Sensitive, Intermediate, Resistant).
Currently, only a subset of species are supported by this task.
Supported Species
The following table shows the species name and the associated NCBI Code. If you are running AMR Search as part of TheiaProk and TheiaEuk, these codes will be automatically determined based on the GAMBIT predicted taxon, or the user-provided expected_taxon input.
| Species | NCBI Code |
|---|---|
| Neisseria gonorrhoeae | 485 |
| Staphylococcus aureus | 1280 |
| Salmonella Typhi | 90370 |
| Streptococcus pneumoniae | 1313 |
| Klebisiella | 570 |
| Escherichia | 561 |
| Mycobacterium tuberculosis | 1773 |
| Candida auris | 498019 |
| Vibrio cholerae | 666 |
| Campylobacter | 194 |
Outputs:
- JSON Output: Contains the complete AMR profile, including detailed resistance state, detected resistance genes/mutations, and supporting BLAST results.
- CSV & PDF Tables: An incorporated Python script,
parse_amr_json.py, extracts and formats results into a CSV file and PDF summary table for easier visualization.
amr_search Technical Details
| Links | |
|---|---|
| Task | task_amr_search.wdl |
| Software Source Code | AMRsearch on GitHub |
| Software Documentation | AMRsearch on GitHub |
| Original Publication(s) | PAARSNP: rapid genotypic resistance prediction for Neisseria gonorrhoeae |
Outputs¶
| Variable | Type | Description |
|---|---|---|
| amr_results_csv | File | CSV formatted AMR profile |
| amr_results_pdf | File | PDF formatted AMR profile |
| amr_search_docker | String | Docker image used to run AMR_Search |
| amr_search_results | File | JSON formatted AMR profile including BLAST results |
| amr_search_version | String | Version of AMR_Search libraries used |
| amr_search_wf_analysis_date | String | Date of analysis |
| amr_search_wf_version | String | Version of PHB used for analysis |