Can we polish the assembly with long reads too?

Yes. In this tutorial, we only polish the assembly with the short reads. This may be enough for bacterial genomes. However, for an even better polish (usually), a common approach is to also polish the assembly with the long reads. A typical workflow for this would assemble with long reads, then polish with long reads (x 4 rounds, with Racon), polish with long reads again (x 1 round, with Medaka), then polish with short reads (x2 rounds with Pilon).

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