PAG Highlights and Workshop Recording: Generating High-Quality Bacterial, Plant and Animal Genomes
Thursday, February 7, 2013
It was great to visit sunny San Diego for the International Plant and Animal Genome meeting last month. We were impressed with the quality of talks and posters, and we appreciated all the scientists who stopped by our booth or attended our workshop.
One highlight for us was listening to Kim Worley from Baylor’s Human Genome Sequencing Center as she described a sooty mangabey primate genome project. Sooty mangabey is a model organism for HIV research, since this particular primate can be infected with the immunodeficiency virus and never develop any symptoms. Because this resistance likely comes from a complex interaction across the immune system rather than a single gene, it was very important for her team to upgrade their draft mangabey assembly, which had gaps representing about 7% of the genome. Worley and her team used PacBio® long reads in conjunction with their own assembly tool, PBJelly, to perform gap-by-gap assembly to fill or reduce those gaps. The effort succeeded in closing 64% and improving another 19% of the gaps. PBJelly can be used with any genome and any type of existing sequence data, Worley noted. Read more about the tool in this paper.
Check out Worley’s presentation and others from our Plant & Animal Genome workshop:
- Introduction: Generating High-Quality Bacterial, Plant and Animal Genomes
Jonathan Bingham, Pacific Biosciences
- Using PacBio Reads and PBJelly Software to Improve Genomes: A Cost-effective Approach to Finishing
Kim C. Worley, Ph.D., Human Genome Sequencing Center, Baylor College of Medicine
- Solving Genetically Complex Problems with Long Reads and Novel Bioinformatics Approaches
Jason Chin, Ph.D., Pacific Biosciences
Also, our team presented two posters describing benefits of the latest chemistry and software releases for the PacBio RS:
- Towards Finishing Genome Assemblies using SMRT® Sequencing
Jenny Gu, Ph.D., Pacific Biosciences
- Greater than 10 kb Read Lengths Routine when Sequencing with Pacific Biosciences’ XL Release
Cheryl Heiner, Pacific Biosciences
We will be attending PAG Asia in March and look forward to seeing you in Singapore!