Question: Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver
2
gravatar for gabri
2.2 years ago by
gabri50
gabri50 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 2.2 years ago by sutturka150 • written 2.2 years ago by gabri50
3
gravatar for lh3
2.2 years 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 2.2 years 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 2.2 years ago by gabri50
3
gravatar for sutturka
2.2 years ago by
sutturka150
USA
sutturka150 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 2.2 years ago by sutturka150

Thanks for your answer, It was really useful!

ADD REPLYlink written 2.2 years ago by gabri50
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