README.md

Workflow overview

A Snakemake workflow for the post-processing of microbial genome assemblies.

1. Parse samples.csv table containing the samples's meta data (python)
2. Annotate assemblies using one of the following tools:
   1. NCBI's Prokaryotic Genome Annotation Pipeline (PGAP). Note: needs to be installed manually
   2. prokka, a fast and light-weight prokaryotic annotation tool
   3. bakta, a fast, alignment-free annotation tool. Note: Bakta will automatically download its companion database from zenodo (light: 1.5 GB, full: 40 GB)
3. Create a QC report for the assemblies using Quast
4. Create a pangenome analysis (orthologs/homologs) using Panaroo
5. Compute pairwise average nucleotide identity (ANI) between the assemblies using FastANI and plot a phylogenetic tree based on the ANI distances.

Running the workflow

Input data

This workflow requires fasta input data. The samplesheet table has the following layout:

sample	species	strain	id_prefix	file
EC2224	"Streptococcus pyogenes"	SF370	SPY	assembly.fasta
...	...	...	...	...

Note: Pangenome analysis with Panaroo and pairwise similarity analysis with FastANI requires at least two samples.