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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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failed circularisation #25

Closed hbadrane closed 2 years ago

hbadrane commented 2 years ago

What if the contig is not circular? like just a chromosome... How to be able to proceed without having to circularize?

rrwick commented 2 years ago

If your replicon is linear, then use the --linear option for the trycycler reconcile and trycycler consensus steps. That will make it skip any circularisation-related steps in the process.

If your replicon might be linear, but you're not sure, I'd recommend running trycycler dotplot (see here). If all the contigs in the cluster are starting/ending at the same place, that's a decent clue that you've got a linear replicon.

Ryan