[jpummil]

Apologies, attached is Quast report comparing base Canu assembly, Base + Quiver polishing, and Quiver + Pilon....

Note, still using --glimmer for gene finding in Quast. Need to switch over to GeneMark-ES (soon).

[ro2006]

Basic workflow using the data you have and the latest versions of software installed using pitchfork:
bax.h5 -> bax2bam -> reads.bam
reads.bam + reference.fasta -> pbalign -> aligned_reads.bam
aligned_reads.bam -> variant_caller (quiver or arrow) -> consensus.fasta

Hi everybody,
I hope my question is not too naive, but I'm quite new to the De Novo assembly. I did a De Novo assembly starting from PacBio reads using Canu.
Now I should polish the assembly and perform variant calling using arrow. My question is: in order to run pbalign as mentioned above, what's your reference.fasta file from the Canu output? Would this be the Contigs.fasta file?
Thanks in advance for any help

[gconcepcion]

Hi everybody,
I hope my question is not too naive, but I'm quite new to the De Novo assembly. I did a De Novo assembly starting from PacBio reads using Canu.
Now I should polish the assembly and perform variant calling using arrow. My question is: in order to run pbalign as mentioned above, what's your reference.fasta file from the Canu output? Would this be the Contigs.fasta file?
Thanks in advance for any help

Yes, the contigs.fasta that is output from Canu is what you want to `polish` so you will select that as your `reference.fasta` to which you map your raw reads using pbalign. Then variantCaller can subsequently call consensus for each base in your reference.fasta based on the raw read coverage