Question: Using HiCanu assembler on PacBio Hifi reads
0
gravatar for pablo
4 months ago by
pablo160
pablo160 wrote:

Hello,

I'm going to use HiCanu on PacBio reads. I already generated the CCS (consensus sequences) , I converted that ccs.bam file into a ccs.fa file .

I would like to know if my command line looks great :

canu -assemble -p assembly -d pacbio genomeSize=1200m -pacbio-hifi ccs.fa

Do I need to inform the -assemble setting , or not? Considering that I already have corrected -correct and trimmed -trim reads.

Bests

EDIT : I got the results when I use the command line I showed you.

I have : 11047 contigs, for an assembly of 2.2 Gb. The expected genome size is around 1.135 Gb . The N50 is 5Mb.

I also tried hifiasm, I have ~1000 contigs, for an assembly of 1.9 Gb. The N50 is >9Mb . So, it is better with that assembler.

Sould I use HiCanu without the -assemble option , and run it like that ? :

canu -assemble -p assembly -d pacbio genomeSize=1200m -pacbio-hifi ccs.fa

Thanks

pacbio ccs hicanu • 659 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by pablo160

I haven't tried HiCanu in several months, so not sure if settings have changed to advise you (it was a development branch I was using at the time). You can also try hifiasm (https://github.com/chhylp123/hifiasm) first to get an idea of what HiCanu might give you before you optimize the settings for HiCanu.

ADD REPLYlink written 4 months ago by jean.elbers1.5k

I already tried hifiasm first, that's why I would like to try HiCanu now. In order to have a comparison of the two assemblies.

ADD REPLYlink written 4 months ago by pablo160

When I tested HiCanu, the following command work:

canu -p assembly -d pacbio genomeSize=1200m -pacbio-hifi ccs.fa

But I guess it doesn't matter with '-assemble' or not, since HiCanu should not have trim/correct steps for HiFi reads. BTW, from your results, do you think hicanu is better or hifiasm is better?

ADD REPLYlink written 4 months ago by hcheng50

I tried both assemblers on several data and all the time, I get better assemblies with hifiasm.

ADD REPLYlink written 4 months ago by pablo160

HiCanu is certainly customizable for assemblies- I didn't get good results with the default settings when I tried it several months ago on a development branch, but it can generate amazing assemblies by tweaking the settings. The same goes for "normalCanu".

ADD REPLYlink written 4 months ago by jean.elbers1.5k

what kind of settings ?

ADD REPLYlink written 5 weeks ago by Picasa590

I am not sure, most likely the error rate settings. Maybe I should have said but others have used it to generate amazing assemblies by tweaking the settings

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by jean.elbers1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1035 users visited in the last hour
_