monkeypox-dynamics:

phylodynamic estimation of 2022 mpox outbreak parameters

analysis workflow

data preparation

1. clone nexstrain monkeypox build | my fork
2. fetch data from nextstrain.org
3. modify filter rules in config/snakemake files

see details in monkeypox-build

4. run nextstrain workflow to produce alignment.fasta and metadata.tsv
5. mask invariant sites from alignment file
   • modify mask rule in config file to accept new BED file
6. re-run nextstrain workflow using identical subsample-seed
7. reformat alignment.fasta strain names as name_location_date

xml preparation using BEAUTI (v. 1.10.4)

1. import descriptive alignment.fasta
2. infer tip dates
3. non-default model parameters:
   • SITES/site heterogeneity model: gamma
   • TREES/tree prior: coalescent bayesian skyline
   • PRIORS/clock.rate: uniform prior with lower 0, upper 1.0, initial 6E-5
   • MCMC/length of chain: 50000000
   • MCMC/log parameters every: 25000
4. export hmpxv_skyliine.xml
5. delete 'trait' block containing 'strictClockBranchRates'

run coalescent bayesian skyline model using BEAST (v. 1.10.4)

plot skyline using TRACER (v. 1.7.2)

run coalescent logistic growth model using BEAST (v. 1.10.4)

XML preparation

• SITES/site heterogeneity model: gamma
• TREES/tree prior: coalescent logistic growth model
• PRIORS/clock.rate: uniform prior with lower 0, upper 1.0, initial 6E-5
• MCMC/length of chain: 50000000
• MCMC/log parameters every: 25000

Export hmpxv_skyline_logistic.xml. Delete 'trait' block containing 'strictClockBranchRates'. Reformat 'gammaPrior' block as 'uniformPrior'.

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export logistic.t50 tsv and parameters treeModel.rootHeight, logistic.growthRate

see /scripts for running BEAST and upstream analysis of output files