mmolari/structural-evo

Analysis of structural microbial genome evolution using pangraph

structural diversity of microbial genomes

This repository contains a snakemake pipeline to analyze the structural diversity of microbial genomes using PanGraph. The pipeline is a simplified version of the one used for the analysis of E. coli ST131 genomes in this preprint.

The input consists of a set of genbank files, containing each a single record (the bacterial chromosome) forming a collection of elements that can be meaningfully structurally compared.

setup

conda environment creation

The pipeline requires a working installation of conda or mamba. To run, it requires an environment with snakemake (v.7+). This can be created with:

conda create -n snakemake -c conda-forge -c bioconda snakemake=7

input data

A new dataset can be added with the following three steps:

• all input data files can be placed in the data/gbk/{acc}.gbk directory, where {acc} is an id of the record (e.g. accession number).
• in addition, a file datasets/{dataset_name}/acc_nums.txt should contain a list of ids for all entries of the dataset. Here {dataset_name} is the name of the dataset.
• finally, update the config.yaml file by adding the new dataset name under the datasets key.

  datasets:
    {dataset_name}:
        guide-strain: "{acc}"

  In addition you must specify the id of a guide-strain from the dataset. This will be used as a reference for the structural comparison.

running the pipeline

After activating the environment with:

conda activate snakemake

You can run the pipeline on a cluster with SLURM workload manager with:

snakemake all --profile cluster

Or alternatively on your local machine with:

snakemake -c <n. cores> --use-conda all