Simulate OC43 lineage A sequence data using SANTA-SIM

Executing the Snakefile will use the SANTA-SIM config files to run SANTA-SIM, format the output into a .fasta file that is compatible with Augur, and use Augur to build a phylogenetic tree and produce an Auspice .json file for visualization.

The Snakefile assumes santa.jar is located at ../../../../santa-sim/dist/santa.jar.

New simulation parameters can be specified by creating a new .xml config file inside the config/ directory. SANTA-SIM config files should be named oc43arep_SCHEME.xml where SCHEME is a unique name for the config file. The config file should save SANTA-SIM output to data/simulated_{gene}_oc43a_SCHEME.fasta. Add SCHEME to the list SCHEME = [] at the top of the Snakefile.

Existing simulation schemes: | scheme | pos_selection | recombination | mutation_rate | exp_dep_penalty | rep_parameters | purifying_parameters | |——–|—————|—————|—————|—————–|—————–|———————————————————————–| | s1 | None | None | 1E-4 | 0 | clonal | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.8, 0.7 | | s2 | Low | None | 1E-4 | 0.03 | clonal | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.97, 0.1, fluctuate 0.001 | | s3 | Moderate | None | 1E-4 | 0.05 | clonal | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.95, 0.1, fluctuate 0.001 | | s4 | High | None | 1E-4 | 0.1 | clonal | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.9, 0.1, fluctuate 0.001 | | s5 | None | Low | 1E-4 | 0 | 0.001, 0.000001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.8, 0.7 | | s6 | Low | Low | 1E-4 | 0.03 | 0.001, 0.000001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.97, 0.1, fluctuate 0.001 | | s7 | Moderate | Low | 1E-4 | 0.05 | 0.001, 0.000001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.95, 0.1, fluctuate 0.001 | | s8 | High | Low | 1E-4 | 0.1 | 0.001, 0.000001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.9, 0.1, fluctuate 0.001 | | s9 | None | Moderate | 1E-4 | 0 | 0.01, 0.00001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.8, 0.7 | | s10 | Low | Moderate | 1E-4 | 0.03 | 0.01, 0.00001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.97, 0.1, fluctuate 0.001 | | s11 | Moderate | Moderate | 1E-4 | 0.05 | 0.01, 0.00001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.95, 0.1, fluctuate 0.001 | | s12 | High | Moderate | 1E-4 | 0.1 | 0.01, 0.00001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.9, 0.1, fluctuate 0.001 | | s13 | None | High | 1E-4 | 0 | 0.1, 0.0001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.8, 0.7 | | s14 | Low | High | 1E-4 | 0.03 | 0.1, 0.0001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.97, 0.1, fluctuate 0.001 | | s15 | Moderate | High | 1E-4 | 0.05 | 0.1, 0.0001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.95, 0.1, fluctuate 0.001 | | s16 | High | High | 1E-4 | 0.1 | 0.1, 0.0001 | rdrp/spike-nonepitope:0.8, 0.7 s1-epitope: 0.9, 0.1, fluctuate 0.001 |