Using HiCanu assembler on PacBio Hifi reads

Question

[pablo]

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

[jean.elbers]

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.

[pablo]

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.

[hcheng]

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?

[pablo]

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

[jean.elbers]

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".

[Picasa]

what kind of settings ?

[jean.elbers]

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