use in hybrid assembly

[phiweger]

Is it a good idea to use Ococo as a long-read assembly polishing tool?

I.e. assemble w/ e.g. Canu, and then map Illumina reads to that assembly, having Ococo compute the consensus.

Thanks

[karel-brinda]

I have never tested Ococo in this use case. My guess is that the main issue would be indels – there are likely to be many in the input, but Ococo will call only SNPs. If you are going to test that, I will be very interested in the results.