Snakemake workflow for Illumina bacterial assembly and QC v1.0.1

<p>This Illumina bacterial assembly snakemake repo is a snakemake workflow to assemble bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification, installation instructions provided in the README). The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/illumina-bacterial-assembly-snakemake and was updated to v1.0.1 with interactive and printer-friendly HTML and PDF reports summarising all QC metrics of reads and assemblies, tool versions used and a graphical workflow overview.</p>