domains / families / science / outbreak-pipeline

outbreak-pipeline

separate

Orchestrates genomic-epidemiology outbreak investigation from pathogen isolates to transmission networks, forking bacterial (snippy -> Gubbins recombination-masking -> IQ-TREE -> TreeTime -> TransPhylo) vs viral (Nextstrain/augur), with parallel MLST typing (cgMLST delegated to epidemiological-genomics/pathogen-typing) and AMR surveillance. Use when committing ONE reference genome for SNP calling (every isolate and distance inherits its coordinates), applying MANDATORY Gubbins recombination-masking on core.full.aln before the tree for recombining bacteria (skipping it inflates the clock 2-5x), gating time-scaling on a temporal-signal test (TempEst R2 >= 0.3), using a pathogen- AND population-specific cluster threshold rather than a universal SNP cutoff, or pinning pangolin-data/Nextclade/Freyja versions for the viral route. Hands mechanism to the epidemiological-genomics component skills; not a re-teach of any single step.

When to use

• genomic-epidemiology outbreak investigation
• transmission networks
• bacterial SNP phylogeny
• viral Nextstrain/augur workflow
• MLST typing
• AMR surveillance
• TreeTime time-scaled tree construction
• TransPhylo transmission inference

When not to use

• re-teach of any single step
• mechanism details of component skills

Skill page

Source