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Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.

The problem

Long-read assembly has come a long way in the last few years, and there are many good assemblers available, including Canu, Flye, Raven and Redbean. Since bacterial genomes are relatively simple (not too large, not too many repeats), a completed assembly (one contig per replicon) is often possible from a long-read set.

But how can you be sure that your long-read assembly is as good as possible?

(Example with multiple different assemblies of the same read set. Each looks fine on its own, but when compared to a reference we can see medium-sized mistakes in each. But crucially, the mistakes are not all in the same place! So none of these assemblies is as good as possible, but together they have the potential to better.)

The solution

(Explain roughly how Trycycler works.)

(Show Trycycler version of the example genome - doesn't have any of the mistakes).