Snakemake workflow for bacterial assembly QC update v1.0.1

This repository contains a Snakemake bacterial assembly QC workflow to perform quality control on assembly files. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries. It will also output PDF and HTML reports with a summary and plots of all tools in the pipeline for all samples. The latest version of the scripts can be found at https://gitlab.ilvo.be/stevebaeyen/bacterial-assembly-qc-snakemake.