Sequencing data analysis for the "Co-evolution of four bacterial species reduces facilitative interactions" paper

This repository hosts the code for the sequencing data analysis. The experiment described in the paper was followed using DNA short-read, DNA long-read and RNA short-read sequencing data.

Environment

The conda environment containing most of the software used for data analysis is exported in environment.yml

Data processing

The genomic short-read and long-read data was processed using a Snakemake workflow.
They can be found in the following directories:

• Illumina: scripts/workflows/illumina
• PacBio: scripts/workflows/pacbio

The RNA sequencing data was analyzed usign RASflow workflow.

Data analysis

Variants and other information relevant for the analysis was parsed and stored ad dataframes in the variants directory.
Below is an outline of the most important dataframes:

• variants/variants_comp_mapping.csv contains all filtered variants for the genomic Illumina data
• variants/{at,ct}_variants_annotations.csv same as above, but additionally with genomic annotations for Ct and At
• variants/snps_freebayes_comp_mapping.csv contains all fixated variants for the genomic Illumina data
• variants/snps_pacbio.csv contains all SNPS in the genomic PacBio data
• variants/assembly_length.csv assembly lenghts for PacBio assemblies

The code for the figures can be found in scripts/diversity.py for variant analsysis and scripts/deletions.py for PacBio data.