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karel-brinda / ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
https://arxiv.org/abs/1712.01146
MIT License
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use in hybrid assembly #37

Open phiweger opened 5 years ago

phiweger commented 5 years ago

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 commented 5 years ago

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.