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This repository contains a Snakemake workflow tailored for assembling bacterial genomes from long-read data generated with R10.4.1 simplex reads from Oxford Nanopore Technologies and includes several QC steps on the resulting assemblies.
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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.
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