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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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Inquiry #53

Closed songmj86 closed 1 year ago

songmj86 commented 1 year ago

Hi

I would like to ask whether trycycler is applicalbe on short-read-assembled contigs as I have multiple contigs assembled from different assemblers and they are originated from illumina hiseq data.

I am looking forward to hearing you

Thanks!

rrwick commented 1 year ago

Sorry, but Trycycler is only appropriate for genomes which can be completed, i.e. each replicon can be assembled into a single contig. And for short-read data, that is almost certainly not the case - your assembly will be fragmented.

However, if your genome can be completed with short-read data (e.g. a viral genome or a very simple bacterial genome), then Trycycler might be possible. But I haven't tried myself!

Ryan