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Scripts and notebooks for the paper: https://doi.org/10.5194/egusphere-2024-2082

A comprehensive Snakemake workflow for assembling high-quality bacterial genomes from Oxford Nanopore long-read sequencing data. The pipeline integrates Autocycler consensus assembly with multiple assemblers (Canu, Flye, Plassembler), performs quality control with Filtlong and Porechop, applies Racon polishing, and provides comprehensive quality assessment using QUAST, BUSCO, and CheckM2. All steps are containerized with conda environments for reproducible results. They include automated HTML/PDF/TXT reporting.