Fig. 1
From: Streamlining whole genome sequencing for clinical diagnostics with ONT technology
Comparison of bacterial whole-genome analysis: conventional versus RapidONT workflows. Conventional workflow: Obtaining complete genomes using the conventional workflow involves the use of different DNA extraction protocols and extensive manual interventions during the de novo assembly process. A total of 89 sequencing datasets, generated by both ONT and Illumina platforms, were de novo assembled using CCBGpipe and Unicycler, respectively. The CCBGpipe assemblies underwent a serial polishing process, and the polished contigs were used as references for completeness evaluation. Unique circular contigs generated by Unicycler, following plasmid validation, were integrated into the CCBGpipe results. The final complete circular genomes were polished twice with POLCA. The RapidONT workflow is a simplified approach. It uses a universal DNA extraction protocol, followed by de novo assembly and a basic assembly polishing process, minimizing the need for manual intervention.
