SMRT Link 7.0 - HGAP

cement_head · 10-03-2019, 01:54 PM

Has anyone gotten the HGAP assembler to work? It seems that it just barfs at different places constantly. Doesn't seem to be very robust at all.

I've used CANU before, so I'm going to try to go back to that...

What about the wtdbg2assembler?

---------------------------------------------------------------------

My mistake - a corrupted downloaded data file was the culprit; should have checked the mdm5 checksum before starting!

SNPsaurus · 10-03-2019, 02:34 PM

What kind of genome are you trying to assemble? I usually go with flye as a first pass (fast, memory efficient) and then Canu if flye underperforms (they seem to trade off which gives a better assembly in our hands). wtdbg2 is fun to try a quick check but I don't think it is as feature complete as flye or canu.

cement_head · 10-06-2019, 07:09 AM

Quote:

Originally Posted by SNPsaurus

What kind of genome are you trying to assemble? I usually go with flye as a first pass (fast, memory efficient) and then Canu if flye underperforms (they seem to trade off which gives a better assembly in our hands). wtdbg2 is fun to try a quick check but I don't think it is as feature complete as flye or canu.

Well, figured it out - was a corrupted file from the download!

Wood Frog Genome - 6 Gbp

Got it working, but it barfs as it wants to fo a 30x coverage and from the RAW reads, it comes up a few thousand short. Would the SEED COVERAGE parameter (in the Advanced tab) be the one I would want to change? From say 30 to 25? (Just to get a rough assembly?) I'm waiting on HiSeq data to do a combined ONT + Pac Bio + HiSeq assembly in CANU.

SNPsaurus · 10-06-2019, 10:08 AM

Oh my, that's a big one. How much memory is it using?

If you just want a rough assembly, I would do wtdbg2 as you can get a sense of contig lengths without consensus generation. I've done flye with 10X read coverage (to look at how much is chloroplast and bacteria in a dirty sample) and it didn't protest. Sorry, haven't used HGAP.

cement_head · 11-19-2019, 05:45 AM

Well, finally got version 8 installed. It never completes, just hangs forever. Seems like a terrible assembler.

lilou · 11-22-2019, 11:35 AM

Hello
HGAP does not support this size of genome. It is made for <=3Gb genomes.
Best to use Falcon which is also a diploid aware assembler

cement_head · 12-04-2019, 07:56 PM

Quote:

Originally Posted by lilou

Hello
HGAP does not support this size of genome. It is made for <=3Gb genomes.
Best to use Falcon which is also a diploid aware assembler

Interesting. HGAP4 Manual doesn't mention this, but the FALCON GitHub repo does - the impression that SMRTLink software gives is that it is a GUI wrapper for FALCON. I guess not. Thanks.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
HGAP assembly through Amazon (smrt analyses)	tony_mane	Pacific Biosciences	1	09-25-2017 04:24 AM
HGAP.3 protocol in the SMRT 2.3 --failing	rachita	Pacific Biosciences	8	08-22-2016 01:17 PM
Help: de novo assembly using SMRT portal and hgap.3	nwfungi	Pacific Biosciences	6	03-01-2016 01:09 PM
Diary: Assembly in SMRT Portal 2.1.1 with HGAP+CA 8.1	pag	Pacific Biosciences	20	09-06-2014 10:20 AM
HGAP Parameters in SMRT Analysis	bonifera	Pacific Biosciences	7	10-24-2013 02:10 PM

10-03-2019, 01:54 PM	#1
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	SMRT Link 7.0 - HGAP Has anyone gotten the HGAP assembler to work? It seems that it just barfs at different places constantly. Doesn't seem to be very robust at all. I've used CANU before, so I'm going to try to go back to that... What about the wtdbg2assembler? --------------------------------------------------------------------- My mistake - a corrupted downloaded data file was the culprit; should have checked the mdm5 checksum before starting! Last edited by cement_head; 10-06-2019 at 07:12 AM. Reason: correction

10-03-2019, 02:34 PM	#2
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	What kind of genome are you trying to assemble? I usually go with flye as a first pass (fast, memory efficient) and then Canu if flye underperforms (they seem to trade off which gives a better assembly in our hands). wtdbg2 is fun to try a quick check but I don't think it is as feature complete as flye or canu. __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

10-06-2019, 10:08 AM	#4
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	Oh my, that's a big one. How much memory is it using? If you just want a rough assembly, I would do wtdbg2 as you can get a sense of contig lengths without consensus generation. I've done flye with 10X read coverage (to look at how much is chloroplast and bacteria in a dirty sample) and it didn't protest. Sorry, haven't used HGAP. __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

11-19-2019, 05:45 AM	#5
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	Well, finally got version 8 installed. It never completes, just hangs forever. Seems like a terrible assembler.

11-22-2019, 11:35 AM	#6
lilou Junior Member Location: switzerland Join Date: Feb 2011 Posts: 1	Hello HGAP does not support this size of genome. It is made for <=3Gb genomes. Best to use Falcon which is also a diploid aware assembler