Autocycler Consensus and Hybrid-Polished Genome Reconstruction

Select short-read or hybrid assembly strategies according to the data available for each isolate.

Run Shovill or SPAdes to generate a bacterial short-read assembly and explain the de Bruijn graph model behind it.

Generate multiple complete long-read assemblies with different assemblers and read subsets for use as Autocycler inputs.

Run the Autocycler consensus workflow and explain how compression, clustering, trimming, resolution, and combination produce a consensus assembly.

Inspect Autocycler cluster metrics and graphs to decide whether automatic resolution is trustworthy or manual review is required.

Polish an Autocycler consensus assembly with Polypolish and verify the short-read-supported corrections.

Run QUAST and CheckM2 and apply an assembly-acceptance rubric to the resulting quality metrics.