Polishing genome with pacbio reads

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4.7 years ago

star715 ▴ 50

Hi, I am trying to assemble some genomes from pacbio reads using HGAP3 followed by quiver polishing. However, even after multiple rounds of quiver polishing, I cannot attain quality value 50 (QV50) for a genome.

QV50 seems to be recommended and I am able to get upto QV30 only. I have done polishing for almost 15 times already. I have tried polishing with different parameter changes like subread length cutoff and blasr maximum divergence.

Can anyone suggest me on how I can achieve an assembled genome of QV50 value?

Thank you

quiver pacbio Assembly • 1.2k views

ADD COMMENT • link 4.7 years ago by star715 ▴ 50

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Why are you using quiver and not the newer arrow out of interest ? Often illumina polishing with pilon or similar is needed after pacbio sequencing.

Which genomes ? Bacteria?

ADD REPLY • link 4.7 years ago by colindaven 7.0k

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Because the data is RSII and arrow does not seem to support it. Yes it is a bacterial genome

ADD REPLY • link 4.7 years ago by star715 ▴ 50

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Hmm then maybe try public (?) illumina reads with pilon ?

Racon or ntedit are other possibilities,

ADD REPLY • link 4.7 years ago by colindaven 7.0k

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