Question: Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver
1
gravatar for gabri
12 months ago by
gabri20
gabri20 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 12 months ago by sutturka120 • written 12 months ago by gabri20
3
gravatar for lh3
12 months ago by
lh330k
United States
lh330k 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 12 months ago by lh330k

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

ADD REPLYlink written 12 months ago by gabri20
3
gravatar for sutturka
12 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 12 months ago by sutturka120

Thanks for your answer, It was really useful!

ADD REPLYlink written 12 months ago by gabri20
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