Aug 6th, 2022
8:00 am - 5:00 pm
Instructors: Abigail Stack, Kacie Quello, Andrew J. Gitto, Owen H. Hudson, Joshua L. Konkol
Organizers: Pei-Ling Yu, Jeremy T. Brawner
Plant Pathologists who are interested in utilizing third-generation sequencing to: study plant or pathogen genome structure and function, aid with plant disease diagnosis or emerging infectious diseases, and general microbiome analysis.
Participants will be led through a hands-on workshop to gain experience with third-generation sequencing using a nanopore sequencer. Using samples we provide, attendees will be guided through the processes of library preparation, flow cell loading, sequencing, data processing and analysis. Participants will learn how changes in DNA yield, purity, and integrity impact nanopore sequencing. Bioinformatic pipelines for base calling, quality control and genome assembly will be shared with participants. We believe that attendees will benefit from this introductory level course, and it will allow researchers to apply this tool to their specific interests, such as targeted sequencing, generating full-length transcripts, and metagenomic applications.
Who: This workshop is aimed at Plant Pathologists interested in applying nanopore sequencing to their own research. Attendees are expected to be familiar with basic laboratory techniques such as pipetting liquids using a micropipette and general lab safety.
Where: This in-person workshop will take place in 403-405, David L. Lawrence Convention Center, Pittsburgh, Pennsylvania.
When: Aug 6th, 2022, 8:00 am - 5:00 pm Eastern time.
Requirements: Participants must bring a personal computer with Windows, MacOS or Linux operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages listed here installed on their computer. All the workshop materials can be found in the public respiratory. Participants can review the materials and follow the instructions to install the software (highly recommended) that is required for sequencing and data processing. Attendees will be able to submit new issues in the public respiratory, so all the attendees can contribute to the discussions.
Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.
Contact: Please email plyu@ufl.edu or jeremybrawner@ufl.edu for more information about the content. For technical problems regarding the website, email plyu@ufl.edu.
Please be sure to complete these surveys after the workshop.
| Time | Particulars |
|---|---|
| 08:00 - 08:15 am | Registration |
| 08:15 - 08:30 am | Introduction and Remarks (by Dr. Pei-Ling Yu) |
| Part 1 | Introduction and sample loading |
| 08:30 - 08:50 am | Overview of the nanopore sequencing workflow (by Kacie Quello) |
| 08:50 - 09:10 am | Applications of nanopore sequencing (by Abigail Stack) |
| 09:10 - 09:30 am | Sample multiplexing and case study in Plant Pathology (by Andrew J. Gitto) |
| 09:30 - 09:45 am | Coffee break |
| 09:45 - 10:30 am | Overview of library preparation and demonstration (by Dr. Pei-Ling Yu) |
| 10:30 - 12:00 pm | Hands on - Flow cell loading |
| 12:00 - 01:30 pm | Lunch Break Lunch not provided |
| Part 2 | Data analysis |
| 01:30 - 01:50 pm | Connecting to Hipergator and linux command (by Josh Konkol) |
| 01:50 - 02:10 pm | SLURM and script anatomy (by Josh Konkol) |
| 02:10 - 02:25 pm | An overview of the bioinformatic pipeline (by Owen Hudson) |
| 02:25 - 02:35 pm | Coffee Break |
| 02:35 - 02:55 pm | Overview of sequencing result (by Josh Konkol) |
| 02:55 - 03:30 pm | Basecalling and quality control (by Josh Konkol) |
| 03:30 - 04:45 pm | Genome assembly (by Dr. Pei-Ling Yu) |
| 04:50 - 04:55 pm | Follow up questions during workshop |
| 04:55 - 05:00 pm | Closing remarks (by Dr. Pei-Ling Yu) and Post-workshop survey |
Go to this page for setup instructions.