General Canu assembler question?

[katievigil]

Hi,

I was wondering why Canu would be less accurate at assembling viral genomes with low sequencing read depth? Are most de novo assemblers less accurate with low sequencing depth?

Thanks! Katie

[skoren]

Generally low sequencing depth can be less accurate, especially when you're using noisier data since the consensus would be using fewer reads. If you're using high-accuracy data like HiFi or Duplex, each individual read is already high quality so lower coverage should be more tolerable. The common issue with viral genomes is that they can be diverse in the sample and non-clonal so you end up with a metagenomic assembly.