bio-epidemiological-genomics-transmission-inference

Name: bio-epidemiological-genomics-transmission-inference
Rating: 5 (1 reviews)
Author: bg-szy

Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12

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Updated 14 days ago

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Version Compatibility

Reference examples tested with: TransPhylo 1.4+ (R), outbreaker2 1.2+ (R), phybreak 0.5+ (R), BadTrIP via BEAST 2.7+ package manager, BEASTLIER via BEAST 1.10+, transcluster 1.0+ (R), HIV-TRACE 1.5+, snp-dists 0.8+, ape 5.8+ (R), igraph 1.6+ (R), TreeTime 0.11+, BactDating 1.1+ (R), BEAST 2.7.6+, lofreq 2.1+, deepSNV via Bioconductor 3.18+, pandas 2.2+, BioPython 1.84+.

Before using code patterns, verify installed versions match. If versions differ:

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