bio-workflows-outbreak-pipeline

Name: bio-workflows-outbreak-pipeline
Rating: 5 (1 reviews)
Author: bg-szy

End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.

1stars

Updated 15 days ago

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Version Compatibility

Reference examples tested with: ncbi-amrfinderplus 4.0+, hamronization 1.1+, tb-profiler 6.2+, mlst 2.23+, chewBBACA 3.3+, pangolin 4.3+ (pangolin-data 1.30+), nextclade 3.8+, snippy 4.6+, gubbins 3.3+, clonalframeml 1.13+, IQ-TREE 2.3.6+, TreeTime 0.11+, BEAST 2.7.6+ (BDSKY 1.5+, MASCOT 3.0+, BICEPS), TransPhylo 1.4+ (R), outbreaker2 1.2+ (R), bactdating 1.1+ (R), freyja 1.4+, mob_suite 3.1+, BioPython 1.84+, pandas 2.2+.