SEQanswers - View Single Post - In-dels Illumina vs. PacBio

slumpy42 · 10-17-2015, 07:48 AM

Thanks for all your replies and suggestions.

I am going through the PacBio training webinars and they mention that deletions are the most common form of error in the circular consensus reads, but don't give a rate.

I have a 3.2 Mb genome and roughly 5,000 single base insertions. All look like they are in homopolymers.

@Biran_Bushnell : I assembled with HGAP.3, includes quiver as the final step. Should I run it again with different settings?

@dgscofield : Thanks, I'll try your script and Pilon and send you the before and after stats, if that would be helpful for you.

10-17-2015, 07:48 AM	#5
slumpy42 Junior Member Location: NYC USA Join Date: Apr 2014 Posts: 3	Thanks for all your replies and suggestions. I am going through the PacBio training webinars and they mention that deletions are the most common form of error in the circular consensus reads, but don't give a rate. I have a 3.2 Mb genome and roughly 5,000 single base insertions. All look like they are in homopolymers. @Biran_Bushnell : I assembled with HGAP.3, includes quiver as the final step. Should I run it again with different settings? @dgscofield : Thanks, I'll try your script and Pilon and send you the before and after stats, if that would be helpful for you.