monkeypox-dynamics:

phylodynamic estimation of 2022 mpox outbreak parameters

analysis workflow

data preparation

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

see details in monkeypox-build

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

xml preparation using BEAUTI (v. 1.10.4)

import descriptive alignment.fasta
infer tip dates
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
export hmpxv_skyliine.xml
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