Nextflow Modules
Showing module(s) with keyword "amr"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/argnorm | Process | amr antimicrobial resistance arg antimicrobial resistance genes genomics metagenomics normalization drug categorization | Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD). |
| nf-core/hamronization/abricate | Process | amr antimicrobial resistance reporting abricate | Tool to convert and summarize ABRicate outputs using the hAMRonization specification |
| nf-core/hamronization/amrfinderplus | Process | amr antimicrobial resistance arg antimicrobial resistance genes reporting amrfinderplus | Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification. |
| nf-core/hamronization/deeparg | Process | amr antimicrobial resistance reporting deeparg | Tool to convert and summarize DeepARG outputs using the hAMRonization specification |
| nf-core/hamronization/fargene | Process | amr antimicrobial resistance arg antimicrobial resistance genes reporting fARGene | Tool to convert and summarize fARGene outputs using the hAMRonization specification |
| nf-core/hamronization/rgi | Process | amr antimicrobial resistance arg antimicrobial resistance genes reporting rgi | Tool to convert and summarize RGI outputs using the hAMRonization specification. |
| nf-core/hamronization/summarize | Process | amr antimicrobial resistance reporting | Tool to summarize and combine all hAMRonization reports into a single file |
| nf-core/staphopiasccmec | Process | amr fasta sccmec | Predicts Staphylococcus aureus SCCmec type based on primers. |
| nf-core/staramr/search | Process | amr plasmid mlst genomics | Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases. |