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kensung-lab / hypo

HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies
GNU General Public License v3.0
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Mixing CCS and Illumina #10

Open mbhall88 opened 4 years ago

mbhall88 commented 4 years ago

I have PacBio CCS, Illumina, and Nanopore reads for the one sample.
It is obvious to me from the docs how to mix 2 of these, but is it possible to mix all three? Or, at the least, can I mix the CCS and Illumina?

Ritu-Kundu commented 4 years ago

Hi Michael,

Thanks for using Hypo. Currently, there is no way to mix CCS and Illumina reads. We are currently conducting experiments to figure out what sequence/combination of polishing would yield in better accuracy if multiple types of reads are available.

Before more information is available, if I had CCS reads, I would use only those to polish rather than using Illumina (which suffers from the limitation of wrong and non-uniform mappings because of repeats) or Nanopore (due to their high error rate). Of course, that's assuming that CCS have uniform and good enough coverage.

Nevertheless, we will share the results of the above mentioned experiments as soon as we have them.