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use in hybrid assembly #37

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phiweger opened this issue May 17, 2019 · 1 comment
Open

use in hybrid assembly #37

phiweger opened this issue May 17, 2019 · 1 comment

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@phiweger
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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
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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.

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