MISMS MinION Workshop – Colombia
Training Workshop for the Implementation of MinION Sequencing for Influenza Viruses
February 6-8, 2020
Irotama Resort
Santa Marta, Colombia
Workshop Objective
This three-day workshop, held February 6-8th, 2020 in Santa Marta, Colombia, introduced new technologies and advanced informatics approaches that can be used for infectious disease genomic characterization in resource-limited settings. Using the portable, low-cost Oxford Nanopore MinION sequencing platform, we will introduce the essential laboratory and computational skills required to perform extensive genetic characterization of viral pathogens, using influenza A virus as a primary demonstration. Topics will include sample preparation, bioinformatics, and phylogenetic approaches to characterize newly sequenced sampled against publicly available data.
By the completion of the workshop, attendees were provided access and training to all essential bioinformatics tools required to establish real-time genetic characterization capabilities in their primary laboratories or at field sites using the low-cost Oxford Nanopore MinION sequencing platform. Best practices for implementing these new technologies in research, clinical, and public health laboratories were emphasized.
Instructors/staff:
Johns Hopkins University: Tom Mehoke, Peter Thielen
Fogarty International Center: Martha Nelson, Nidia Trovao
Workshop Agenda
Day 1 (Thursday Feb 6)
Introduction to Genomics Technologies and Oxford Nanopore Sequencing
Time | Event | Presenter |
9:00am | Welcome and Introductions
|
Peter Thielen |
9:30am | Low-Resource Genome Sequencing with Oxford Nanopore: Outbreak response and Influenza Applications | Peter Thielen |
10:00am | Data Analysis Objectives: Rapid Characterization and Consensus Sequence Generation | Peter Thielen |
11:00am | BREAK | |
11:15am | Rapid Talks: Single Slide Presentations from Attendees | Attendees |
12:00pm | Lunch / Surveillance Meeting Field Trips |
Day 2 (Friday Feb 7):
Laboratory Considerations and Basic Bioinformatics
Time | Event | Presenter |
9:00am | Practical Considerations: Establishing a Genomics Wet Laboratory
|
Peter Thielen |
9:30am | Concepts: Optimized Influenza A Virus Sample Preparation with Ligation reagents
|
Peter Thielen |
10:00am | BREAK | |
10:15am | Hands on: Sequencing with the MinION | Peter Thielen |
11:45pm | Data Manipulation and Exploratory Data Analysis
|
Tom Mehoke |
12:15pm | Lunch | |
1:15pm | Introduction to Phylogenetics Concepts
|
Martha Nelson |
2:15pm | Using data produced by the MinION
|
Tom Mehoke |
2:45pm | BREAK | |
3:00pm | Hands-on: Processing data produced so far
|
Tom Mehoke |
5:00pm | Day 2 Review
Revisit data from the earlier sequencing run Recap of topics Post-session evaluations |
Day 3 (Saturday Feb 8):
Phylogenetics
Time | Event | Presenter |
9:00am | Identifying Genomes and Building a Genetic Sequence Dataset
|
Nídia Trovão |
10:00am | Multiple Sequence Alignment and Building a Phylogenetic Tree
|
Nídia Trovão |
11:00am | BREAK | |
11:15am | Post-processing of Phylogenetic Trees
|
Martha Nelson |
12:15pm | Lunch | |
1:15pm | How To: Interpret a Phylogenetic Tree | Martha Nelson |
2:15pm | Final Recap
|
|
3:00pm | BREAK | |
3:15pm | Time to Work With Your Own Data | All instructors available for questions |