Genome assembly using Pacbio sequel data

yjpark1091 · 11-23-2017, 05:17 AM

Hello guys~

I got a fungal genome sequencing data using sequel platform.

Also, I already finish to set up SMRT Link and SMRT analysis to lab server.

The reason why I make new post in pacbio forum is getting an opinion about choosing assemble protocol (HGAP2, HGAP3, HAGP4 ....)

Please tell or suggest me about best assemble protocol if there any guys that assemble fungal genome data from pacbio platform.

Any opinion, source, or comments are okay.
Thank you.

rhall · 11-27-2017, 08:47 AM

HGAP.4, it's actually not possible to run sequel data through the HGAP.2 and HGAP.3 pipelines.
How big is the fungi? so long as you have reasonable coverage default parameters should be a good starting point.

yjpark1091 · 11-27-2017, 04:54 PM

I think it is almost 30 Mb and consist of several chromosome.
The value is also just estimation. Also there is no sequencing report of fungal genome that similar with my fungal genome.
And I already try to analyzed my fungal genome sequel data using HGAP.4 in Pacbio SMRT Link but the result is not good that sum of polish contig is not same with estimate genome size of my fungal genome.
In this case, how can i improve my sequening result?

GenoMax · 11-27-2017, 05:11 PM

Post some of the stats from your HGAP.4 run. Dr. Hall will likely need those to comment further.

rhall · 11-28-2017, 12:13 PM

Preassembled yield, polished contig total size and what the raw coverage of the polished contigs is would be a good place to start.

SNPsaurus · 11-29-2017, 08:32 AM

You could look at completeness by running Busco on it. http://busco.ezlab.org/

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11-23-2017, 05:17 AM	#1
yjpark1091 Junior Member Location: Kyungpook Nat'l Univ. in South Korea Join Date: May 2017 Posts: 3	Genome assembly using Pacbio sequel data Hello guys~ I got a fungal genome sequencing data using sequel platform. Also, I already finish to set up SMRT Link and SMRT analysis to lab server. The reason why I make new post in pacbio forum is getting an opinion about choosing assemble protocol (HGAP2, HGAP3, HAGP4 ....) Please tell or suggest me about best assemble protocol if there any guys that assemble fungal genome data from pacbio platform. Any opinion, source, or comments are okay. Thank you.

11-29-2017, 08:32 AM	#6
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 435	You could look at completeness by running Busco on it. http://busco.ezlab.org/ __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

11-27-2017, 08:47 AM	#2
rhall Senior Member Location: San Francisco Join Date: Aug 2012 Posts: 318	HGAP.4, it's actually not possible to run sequel data through the HGAP.2 and HGAP.3 pipelines. How big is the fungi? so long as you have reasonable coverage default parameters should be a good starting point.

11-27-2017, 04:54 PM	#3
yjpark1091 Junior Member Location: Kyungpook Nat'l Univ. in South Korea Join Date: May 2017 Posts: 3	I think it is almost 30 Mb and consist of several chromosome. The value is also just estimation. Also there is no sequencing report of fungal genome that similar with my fungal genome. And I already try to analyzed my fungal genome sequel data using HGAP.4 in Pacbio SMRT Link but the result is not good that sum of polish contig is not same with estimate genome size of my fungal genome. In this case, how can i improve my sequening result?

11-27-2017, 05:11 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,698	Post some of the stats from your HGAP.4 run. Dr. Hall will likely need those to comment further.

11-28-2017, 12:13 PM	#5
rhall Senior Member Location: San Francisco Join Date: Aug 2012 Posts: 318	Preassembled yield, polished contig total size and what the raw coverage of the polished contigs is would be a good place to start.