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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Canu for shotgun metagenomic assembly of complex environments #2348

Open Hedi65 opened 1 month ago

Hedi65 commented 1 month ago

Dear developer,

I found there are inconsistent opinions across experts. Are you suggesting Canu for assembling metagenomic data from complex environments such as wastewater? If so, what settings should I pay attention to while running Canu?

Thanks

skoren commented 1 month ago

Yes, canu can work for metagenomic datasets as long as you aren't expecting it to maintain phase/reconstruct complete genomes. For high-accuracy data like HiFi you probably want to look at MetaFlye or Metahifiasm instead. The FAQ lists the settings for metagenomics, which essentially tell canu to correct all the input PacBio CLR or ONT data:https://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak