recombinant_phages_study

This repository contains a pipeline used to analyse recombinant phage clones.

More information @ notes

Configuration

• HMM: set the cores available for the HMM algorithm and the parameters of the HMM model used to create the plots

• Optimization of recombination parameter: the optimization of the transition parameter is run independently from the whole pipeline, it consists of several runs of the HMM algorithm over all the clones. At each iteration a different value of transition probability is used and the total log likelihood is saved. The output of the optimization is just a plot that shows the average trend of log likelihood depending on the recombination parameter. The flag parameter is a boolean value that defines if the optimization will be executed or not. The parameter "values" takes comma separated entries for the transition probability.

• Plots: these parameters control the final plot of the pipeline, containing all the clones aligned to the hybrid reference.

  • convolution_window: convolution window applied to the mismatch distribution, affects the resolution of the clone genome line.
  • common_x_axis: not important, probably will be removed
  • interline: space in between lines representing clone genomes
  • thickness: thickness of the line representing the clone genome
  • colors:

Running the pipeline

Local execution

snakemake --profile local all

HPC execution

snakemake --profile cluster all