Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver

Question

[gabri]

Hi!

I have assembled my PacBio FASTQ reads with Canu. Now I would like to polish\correct the assembly by mapping these PacBio FASTQ reads on the assembly itself. I heard about Quiver in the SMRTanalysis pack, but I'm wondering if there is any alternative software.

Thanking you in advance for your help!

Answer 1

[lh3]

Canu uses alignments between pacbio reads to correct away most sequencing errors in raw reads. You can't do much better without using the signal information. To achieve high-quality consensus, Quiver is your only choice.

[gabri]

Thank you very much for the information you gave me. Quiver seems to be the best choice, I will try it!

Answer 2

[sutturka]

The tools Pilon and Icorn2 performs assembly polishing with Illumina data. I am not sure if Icorn2 also takes PacBio reads for correction. Running additional rounds of Quiver may be the helpful to use the PacBio reads efficiently.

[gabri]

Thanks for your answer, It was really useful!