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rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
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Assemblers #9

Closed ranitori closed 3 years ago

ranitori commented 3 years ago

Hi, In your wiki, under the section on assembling the subsets generated by Trycycler you mention Flye, Raven, Can etc. Is there any reason not to use Unicycler for my long-read Nanopore data? Thanks.

rrwick commented 3 years ago

If you're talking about a long-read-only Unicycler assembly, then yes, you could use that. However, the long-read-only approach used by Unicycler is a bit dated (e.g. it uses minimap instead of minimap2). I would instead recommend doing Miniasm/Minipolish assemblies. This is conceptually very similar to what Unicycler does but uses more up-to-date components.

If you also have short reads, then you have the option of doing a hybrid Unicycler assembly, which follows a very different approach. In principle, you could certainly use a hybrid Unicycler assembly as Trycycler input. But I haven't experimented much with this, and my gut feeling is that it's not a great idea. That's because hybrid Unicycler assemblies can sometimes botch repetitive regions, whereas long-read-only assemblies tend not to. So if you do have short reads, I think you're probably better off saving them for a final polish at the end of the Trycycler process. But again, I haven't tested this, so feel free to experiment!

Ryan