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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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Short and long reads from different isolates #289

Closed termithorbor closed 2 years ago

termithorbor commented 2 years ago

Hi,

what would be the best approach for assembling the genome when the short and long reads come from different isolates?

Thanks in advance :)

rrwick commented 2 years ago

Well. my initial answer is don't do that :smile: If the read sets are from different isolates, then I don't expect them to assemble well together!

But if you need to for some reason, I'd try both a short-read-first approach like Unicycler and a long-read-first approach like Trycycler+polishing. A Unicycler assembly will probably look more like the genome in the short-read set, and a Trycycler+polishing assembly may look more like the genome in the long-read set.

For either approach, the closer the two isolates are, the better I'd expect the assembly to work. Good luck!

Ryan