User Group Meeting Agenda- June 17, 2015
University of Maryland School of Pharmacy, 20 N. Pine Street, Room Number PH N103
| Time | Description |
|---|---|
| 8:30 – 9:00am | Breakfast |
| 9:00 – 9:30am | Opening Remarks Kevin Corcoran, Pacific Biosciences |
| 9:30 – 9:55am | Using Long Reads to Improve a Benchmark Human “Genome in a Bottle” Justin Zook, Ph.D., The National Institute of Standards and Technology (NIST) |
| 9:55 – 10:20am | Using PacBio long reads to generate a high quality reference for the allotetraploid Coffea arabica and its maternal diploid ancestor Coffea eugenioides Marcela Yepes, Ph.D., Cornell University |
| 10:20 – 10:45am | Improving Maize Reference Resources with Hybrid Sequencing Approaches Doreen Ware, Ph.D., USDA ARS, Cold Spring Harbor Laboratory |
| 10:45 – 11:25am | Coffee Break |
| 11:25 – 11:50am | Characterization of Fusion Genes and the Significantly Expressed Fusion Isoforms in Breast Cancer by Hybrid Sequencing Kin Fai Au, Ph.D., Department of Internal Medicine and Biostatistics, University of Iowa |
| 11:50 – 12:15pm | Toward Building Niche Diagnostic Assays that Benefit from Targeted Long-read Sequencing Methods Robert P. Sebra, Ph.D., Icahn School of Medicine at Mount Sinai |
| 12:15 – 1:35pm | Lunch - Sponsored by DNAnexus |
| 1:35 – 2:00pm | Construction of Large Insert Target Enrichment Libraries for PacBio Long Read-length Sequencing Mark Wang, Ph.D., Baylor College of Medicine |
| 2:00 – 2:25pm | No Assembly Required: Full-length MHC Class I Allele Discovery by PacBio Circular Consensus Sequencing Mariano Sanchez-Lockhart, Ph.D., United States Army Medical Research Institute of Infectious Disease |
| 2:25 – 2:50pm | Full-length HIV-1 env Deep Sequencing in a Donor with Broadly Neutralizing V1/V2 Antibodies Melissa Smith, Ph.D., Pacific Biosciences |
| 2:50 – 3:30pm | Coffee Break |
| 3:30 – 3:55pm | High Quality Full Length 16s Sequence: A Case Study in Sino-Nasal Biogeography Josh Earl, M.S., Drexel College of Medicine |
| 3:55 – 4:20pm | Deep Sequencing in the Deep Subsurface: De Novo Metagenomic Assembly to Recover Complete Genomes from the Soudan Iron Mine Jon Badalamenti, Ph.D., University of Minnesota |
| 4:20 – 4:30pm | Closing Remarks Kevin Corcoran, Pacific Biosciences |
| 4:30 – 6:00pm | Reception – Sponsored by Sage Science |
| Time | Description |
|---|---|
| 1:00– 1:40pm | Generation of ultra-long sheared DNA fragments >20-kb for large genome assembly applications |
| 1:40– 2:00pm | Barcoding Product Updates: PacBio Barcoded Adapters and Barcoded Universal Primer Kits |
| 2:00– 2:15pm | Whole Transcriptome Iso-Seq™ using Barcodes |
| 2:15– 2:45pm | Coffee Break |
| 2:45– 3:30pm | Targeted SMRT Sequencing Using a Solution-Based Capture & Enrichment Strategy |
| 3:30– 4:30pm | Introduction to SMRT Portal Secondary Analysis Protocols and Reports for Sample QC |
| 4:30– 5:00pm | Open discussion and questions |
Sample Preparation Workshop - June 16, 2015
1:00 – 5:00 PM
Discovery Auditorium, University of Maryland BioPark, Bldg II, 801 W. Baltimore Street
| Time | Description |
|---|---|
| 1:00-2:15pm | Iso-Seq - troubleshooting the SMRT Analysis Iso-Seq pipeline, discussion of tertiary analysis options, including a detailed walkthrough |
| 2:15– 3:30pm | Large Genome Assembly - Software options for large genome assembly, install and setup of FALCON |
| 3:30– 4:00pm | Coffee Break |
| 4:00– 5:00pm | Open discussion, topics provided by attendees |
| Special Guest: Jon Badalamenti, Ph.D., University of Minnesota |
Bioinformatics Workshop – June 16, 2015
1:00 – 5:00 PM
Invent and Advance Conference Rooms, University of Maryland BioPark, Bldg II, 801 W. Baltimore Street
| Time | Description |
|---|---|
| 8:30 – 9:00am | Breakfast |
| 9:00- 10:15am | Iso-Seq - troubleshooting the SMRT Analysis Iso-Seq pipeline, discussion of tertiary analysis options, including a detailed walkthrough |
| 10:15– 11:30am | Large Genome Assembly - Software options for large genome assembly, install and setup of FALCON |
| 11:30– 12:00pm | Lunch |
| 12:00– 1:00pm | Open discussion, topics provided by attendees |
| Special Guest: Sergey Koren, Ph.D., NBACC |
Bioinformatics Workshop – June 18, 2015
9:00 – 1:00 PM
University of Maryland School of Pharmacy, 20 N. Pine Street, Room Number PH N103
Thank you to our sponsors:
