Description

Code to accompany the paper "Inducing Novel Endosymbioses by Bacteria Implantation in Fungi".

Details

bacteria_comparison.py

The snakemake pipeline used to compare bacterial samples.

braker.sh

The job submission script for running BRAKER to annotate the fungus assembly.

fungus_comparison.py

The snakemake pipeline used to compare fungal samples.

illumina_assembly.py

The snakemake pipeline used to independently assemble all bacterial samples.

pacbio_assembly.sh

The job submission script for assembling the fungus Pacbio data.

snp_analysis.r

The R script used to extract information about SNPs occuring over time along the different lineages.

summarise_pile.r

The R script used to check for SNP frequencies over time along different lineages.