Question: Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver
1
gravatar for gabri
18 months ago by
gabri40
gabri40 wrote:

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!

ADD COMMENTlink modified 18 months ago by sutturka120 • written 18 months ago by gabri40
3
gravatar for lh3
18 months ago by
lh331k
United States
lh331k wrote:

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.

ADD COMMENTlink written 18 months ago by lh331k

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

ADD REPLYlink written 17 months ago by gabri40
3
gravatar for sutturka
18 months ago by
sutturka120
USA
sutturka120 wrote:

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.

ADD COMMENTlink written 18 months ago by sutturka120

Thanks for your answer, It was really useful!

ADD REPLYlink written 17 months ago by gabri40
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