Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Question: canu correction process liaoyunshi Bioinformatics 0 07-31-2017 08:54 PM
assembling Nimblegen exome reads rworthi Bioinformatics 4 11-09-2011 11:23 AM
Assembling very large reads k-gun12 Bioinformatics 2 03-12-2011 09:06 AM
454 Reads correction with Short reads ? yvan.wenger Bioinformatics 3 11-26-2010 05:17 AM
Assembling Sanger Reads santhosh003 Bioinformatics 3 04-22-2010 12:54 AM

Thread Tools
Old 05-19-2019, 02:20 AM   #1
Junior Member
Location: Europe

Join Date: May 2019
Posts: 2
Question Assembling raw reads with Canu, but without correction

Hello friends,

I have raw ONP and PacBio reads for the human genome, ecoli, and yeast, and I want to test Canu's performance on them, without correction.

If I understand correctly, I would only execute the assemble step of Canu, and specify -nanopore-raw or -pacbio-raw, depending on the technology.

Is this correct?

Also, what other parameters should I set/tweak to get better accuracy in this scenario? Some candidate parameters I know:
  • rawErrorRate
  • utgOvlErrorRate
  • utgGraphDeviation
  • utgRepeatDeviation
  • utgRepeatConfusedBP

Also, is there a platform where I can ask this to the developers of Canu? Is github/issues the right place for such a question?

Any response greatly appreciated!

Last edited by ekarais; 05-19-2019 at 02:24 AM. Reason: Forgot to add something
ekarais is offline   Reply With Quote
Old 05-21-2019, 05:44 AM   #2
Senior Member
Location: Germany

Join Date: Oct 2008
Posts: 415

Why not just specify -nanopore-corrected to probably make canu skip this stage ?

Also, why would you even want to do this ? You'll get really awful results, the correction is there for a reason.

Also, I think miniasm does rapid assembly on uncorrected reads, but then you have massive problems trying to correct base level errors in the asm afterwards.
colindaven is offline   Reply With Quote
Old 05-21-2019, 02:13 PM   #3
Registered Vendor
Location: Eugene, OR

Join Date: May 2013
Posts: 523

wtdbg2 will overlap long reads and then correct/consensus as a separate step (I know this doesn't help getting Canu to do it that way, just following up on colindaven's comment).

Canu corrects reads before overlapping. I don't know if it can be shoe-horned into working on raw reads since it isn't expecting a 15% error rate when it overlaps. Just to offer additional annoyingly non-Canu advice, the flye assembler constructs an assembly graph before read correction.
Providing nextRAD genotyping and PacBio sequencing services.
SNPsaurus is offline   Reply With Quote

assembly, canu, raw

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:30 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO