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Old 04-22-2018, 11:58 PM   #1
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Location: Kyungpook Nat'l Univ. in South Korea

Join Date: May 2017
Posts: 4
Default Ploidy estimation or decision using pacbio sequel data

Hi all.

After finish assemble fungus genome from pacbio sequel using SMRT link or Falcon assembler, the genome size is twice as much as I expected.

So, I want to get your advice or opinion for estimation or decision of ploidy of Fungal genome from Pacbio Sequel platform.

Actually, the fungus genome was extracted using mycelia and spore.
(I think this is a mistake that I made...)

In my search, most of program for ploidy estimation are focus on short read such as illuminal Miseq and Hiseq.

If there are good opinions or comments, and ideas please tell me about that.

Best regards,

Last edited by yjpark1091; 04-23-2018 at 12:01 AM.
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Old 04-29-2018, 11:46 AM   #2
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Location: Toronto

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Hi there,
I am interested in hearing how you ended up handling this. I suppose I do not have a definitive answer for your question, but any chance that you have a reference to compare to? If you take a closer look at your assembly, it would be interesting to see if you have "duplicated" chromosomes (provided your assembly allows you to make an assessment about chromosomes) as that I think could be indicative of a diploid (or polyploid, etc.) genome.
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diploid, fungus genome, haploid, pacbio, ploidy

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