Question

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

2

Entering edit mode

7.5 years ago

gabri ▴ 60

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!

PacBio Assembly Polish Correct FASTQ • 3.2k views

ADD COMMENT • link updated 7.5 years ago by sutturka ▴ 190 • written 7.5 years ago by gabri ▴ 60

score 3 · Accepted Answer · 2017-06-16

3

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7.5 years ago

lh3 33k

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 COMMENT • link 7.5 years ago by lh3 33k

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

ADD REPLY • link 7.5 years ago by gabri ▴ 60

score 3 · Accepted Answer · 2017-06-16

3

Entering edit mode

7.5 years ago

sutturka ▴ 190

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.