Darwin Bactmap

Mapping of bacterial short reads to a reference genome for SNP calling, phylogenetics, and outbreak analysis. Steps: Step 1: fastqc; Step 2: fastp; Step 3: bwa_mem; Step 4: samtools_sort; Step 5: snippy; Step 6: gubbins; Step 7: multiqc. 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.