November 12th, 2013- PacBio Posts Slides from User Group Meeting
Lance Hepler, Center for AIDS Research, UC San Diego
Hepler used the PacBio RS to study intra-host diversity in HIV-1. He compared PacBio’s performance to that of 454®, the platform he and his team previously used. Hepler noted that in general, there was strong agreement between the platforms; where results differed, he said that PacBio data had significantly better reproducibility and accuracy.
John Huddleston, University of Washington
Huddleston is looking at challenging regions in the human genome, noting
that assembly accuracy needs to be quite high to resolve breakpoints and
reconstruct duplication architectures. His team is working with BACs to
validate the use of the PacBio platform as a faster, more cost-effective
alternative to Sanger. In one study, his team found that PacBio results
had 99.994% identity with Sanger results and showed uniform coverage
across the clone.
Lisbeth Guethlein, Stanford University School of Medicine
Guethlein looked at highly repetitive and variable regions of the
orangutan genome. Guethlein reported that “PacBio managed to accomplish
in a week what I have been working on for a couple years,” (with
Sanger) and the results were concordant.
(LOT More,go to IHUB for link)
More from User Group Meeting
Alex Copeland, DOE – Joint Genome Institute
Copeland offered an overview of the institute’s microbial and fungal reference assembly pipeline, describing their experience with a 10x increase in read length and total throughput in three years on the PacBio platform. He shared that the team has shifted to a PacBio-only pipeline, and that they are finishing genomes on the platform for less than $2,000.