Question: Polishing genome with pacbio reads
0
gravatar for star715
10 months ago by
star71520
star71520 wrote:

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

assembly pacbio quiver • 222 views
ADD COMMENTlink written 10 months ago by star71520

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 REPLYlink written 10 months ago by colindaven2.5k
1

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

ADD REPLYlink written 10 months ago by star71520

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

Racon or ntedit are other possibilities,

ADD REPLYlink written 10 months ago by colindaven2.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2280 users visited in the last hour