Darwin Pathogensurveillance

Whole-genome sequencing-based pathogen surveillance: assembly, typing, AMR detection, and phylogenetics Steps: Step 1: FastQC; Step 2: Read Trimming (fastp); Step 3: Genome Assembly (Shovill); Step 4: Assembly QC (QUAST); Step 5: MLST Typing; Step 6: AMR Gene Detection (RGI/CARD); Step 7: Core Genome Phylogenetics (Snippy+IQ-TREE); Step 8: Surveillance Report. Verticals: microbial_genomics, clinical_genomics.

Use in DarwinOmics

How to use it

Use this workflow element when the submitted analysis needs a multi-step execution path, imported workflow, Darwinomics wrapper, or workflow-scale comparison rather than a single module.