Ploidy estimation or decision using pacbio sequel data

yjpark1091 · 04-22-2018, 11:58 PM

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,
YJ

kramergj · 04-29-2018, 11:46 AM

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.
Glenna

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Genome assembly using Pacbio sequel data	yjpark1091	Pacific Biosciences	5	11-29-2017 09:32 AM
New PacBio system: Sequel	SNPsaurus	Pacific Biosciences	62	09-28-2017 05:33 AM
Pacbio sequel for single cell human WGS?	WhatsOEver	Pacific Biosciences	5	06-27-2017 12:02 PM
variant calling from pacBio Sequel data	splaisan	Bioinformatics	0	03-25-2017 07:20 AM
PacBio Sequel demultiplexing	Ali May	Pacific Biosciences	4	12-06-2016 10:43 PM

04-22-2018, 11:58 PM	#1
yjpark1091 Junior Member Location: Kyungpook Nat'l Univ. in South Korea Join Date: May 2017 Posts: 4	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, YJ Last edited by yjpark1091; 04-23-2018 at 12:01 AM.

04-29-2018, 11:46 AM	#2
kramergj Junior Member Location: Toronto Join Date: Nov 2015 Posts: 3	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. Glenna