Extraction consists of enzymatic degradation of bacterial cell walls followed by an initial DNA extraction in phenol-chloroform. This is followed by a proteinase K and RNase A digestion at high temperature and purification with a gravity column. Finally, small fragments are removed by modified SPRI bead size selection. After sequencing and basecalling, read sequences are assembled twice with varying genomeSize parameter values. These two assemblies are screened for sites not spanned by multiple long reads indicating misassembly, merged, and then circular sequences are identified and trimmed. The consensus sequence is refined by either short-read or long-read polishing, and final assemblies are screened once more for any misassembled sites not spanned by long reads.