Comprehensive Training in Infectious Disease Applications of Next Generation Sequencing

Note: The NGS training has been an overwhelming success, surpassing the number of licenses available. ASM is currently exploring options to increase the number of seats and will provide an update shortly.

Blood Agar petri dish with sequence read coming from bacteria on the plate.
Sequence reads coming off of a petri dish.
Source: American Society for Microbiology
ASM has developed 50 hours of accredited, free training to educate the clinical microbiology (CM) workforce on Next Generation Sequencing (NGS) technologies to increase pathogen genomic sequencing capacity and increase preparedness for the next pandemic through enhanced molecular surveillance. Training was also developed to educate our bioinformatics partners on infectious diseases to enhance their understanding of additional clinical applications and the technology’s impact on public health. 

Training is available for all levels of experience, and learners can choose to build from one level to the next: 

  • Beginner: CM workforce that does not have NGS equipment. 
  • Intermediate: CM workforce that acquired a NGS sequencer during the COVID-19 pandemic
  • Advanced: CM workforce that had NGS experience pre-pandemic and is actively involved in sequencing.
  • Expert: Bioinformatics partners who already work on human genomics and would benefit from education on infectious disease applications of NGS. The content is intermediate and advanced.  

Training will be offered virtually and in-person at ASM Microbe 2023. View the schedule of topics below:

February 2023
Feb. 15, 2023 | Review of Pathogen Genomics (Viruses, Bacteria, Fungi, Parasites)-Part 1
Speaker: Frederic D. Bushman
Audience: Beginner
Webinar, live and recorded

Feb. 16 | Specifics of Bacterial Genomics
Speaker: Shaun Yang
Audience: Intermediate
Webinar, live and recorded


Feb. 22 | Introduction to NGS Infrastructure
Speaker: Amy Mathers
Audience: Intermediate
Webinar, live and recorded


Feb. 27 | Define Different Sequencing Techniques and Platforms
Speaker: Winston Timp
Audience: Intermediate
Webinar, live and recorded

March 2023

March 1 | NGS Library Creation Approaches, Methods and Design
Speaker: Heather Blankenship
Audience: Advanced
Webinar, live and recorded

March 2 | Review of Pathogen Genomics (Viruses, Bacteria, Fungi, Parasites)-Part 2
Speaker: Frederic D. Bushman
Audience: Beginner
Webinar, live and recorded

March 8 | Introduction to Clinical Virology and Viral Genomics
Speaker: P Hemarajata
Audience: Intermediate
Webinar, live and recorded

March 9 | Next-Generation Sequencing in Microbiology: Pathogen and AMR Detection (Part 1)
Speaker: Charles Chiu
Audience: Intermediate
Webinar, live and recorded

March 15 | Next-Generation Sequencing in Microbiology: Pathogen and AMR Detection (Part 2)
Speaker: Charles Chiu
Audience: Intermediate
Webinar, live and recorded

March 16 | Connecting the Genome to Molecular Diagnostics
Speaker: Rosemary She
Audience: Beginner
Webinar, live and recorded

March 22 | Sequence Comparison and Phylogeny
Speaker: Kelly Oakeson
Audience: Advanced
Webinar, live and recorded

March 23 | Specifics of Eukaryotic Genomics
Speaker: Bridget Barker
Audience: Intermediate
Webinar, live and recorded

March 29 | NGS of Cultured Fungal Pathogens
Speaker: Christina Cuomo
Audience: Advanced
Webinar, live and recorded

March 30 | The Evolution of NGS Technologies-Part I
Speaker: Mendy Poulter
Audience: Beginner
Webinar, live and recorded


April 2023
April 5 | The Evolution of NGS Technologies-Part II
Speaker: Mendy Poulter
Audience: Beginner
Webinar, live and recorded

April 6 | Overview of Whole Genome Sequencing
Speaker: Nick Moore
Audience: Beginner
Webinar, live and recorded

April 12 | Antimicrobial Resistance and NGS-1
Speaker: Hannah Gray
Audience: Advanced
Webinar, live and recorded

April 19 | Antimicrobial Resistance and NGS-2
Speaker: Kimberlee A. Musser
Audience: Advanced
Webinar, live and recorded

April 20 | Overview of Amplicon-Based NGS 
Speaker: Paige Larkin
Audience: Beginner
Webinar, live and recorded

April 26 | Maintaining Order in the Sequence Tsunami: Sequence Data Management for Clinical Microbiologist and Bioinformaticians
Speaker: Andrew Warren
Audience: Intermediate
Webinar, live and recorded

April 27 | Overview of Shotgun Metagenomic Sequencing
Speaker: Robin Patel
Audience: Beginner
Webinar, live and recorded

May 2023
May 8 | Application of Genomic Epidemiology for Surveillance and Infection Prevention in Healthcare Settings - Part 1
Speaker: Marie-Claire Rowlinson
Audience: Beginner
Webinar, live and recorded

May 10 | Application of Genomic Epidemiology for Surveillance and Infection Prevention in Healthcare Settings - Part 2
Speaker: Marie-Claire Rowlinson
Audience: Beginner
Webinar, live and recorded

May 11 | Introduction to NGS Data Analysis Workflows
Speaker: Kelsey Florek
Audience: Advanced
Webinar, live and recorded

May 17 | NGS Data Collection and Storage
Speaker: Xiaowu Gai
Audience: Beginner
Webinar, live and recorded

May 18 | NGS Sequence Analysis
Speaker: Julie Hirschborn
Audience: Beginner
Webinar, live and recorded

May 25 | Metagenomic NGS Methods
Speaker: Kevin Chau
Audience: Advanced
Webinar, live and recorded

June 2023
June 1 | Whole Genome Sequencing
Speaker: John Dekker
Audience: Intermediate
Webinar, live and recorded

June 15 | Bacterial or Fungal WGS Bioinformatics
Speaker: Robert Petit
Audience: Advanced
In person at Microbe 2023 and recorded

Hospital Infection Control
Speaker: Shaun Yang
Audience: Advanced
In person at Microbe 2023 and recorded

Bioinformatics with Terra.Bio: Direct-from-Specimen Approaches for Viral Genomic Characterization
Speaker: Frank Ambrosio
Audience: Advanced
In person at Microbe 2023 and recorded

All About Trees: Sequence Comparison and Phylogeny
Speaker: Kelly Oakeson
Audience: Advanced
In person at Microbe 2023 and recorded

Building NGS Data Analysis Workflows
Speaker: Robert Petit
Audience: Advanced
In person at Microbe 2023 and recorded

June 16 | From Start to Finish: Hands-on Design of NGS and Bioinformatics Practice-Part I
Speaker: Stephanie Goya
Audience: Beginner
In person at Microbe 2023 and recorded

June 17 | From Start to Finish: Hands-on Design of NGS and Bioinformatics Practice-Part II
Speaker: Stephanie Goya
Audience: Beginner
In person at Microbe 2023 and recorded

June 18 | Introduction to NGS Public Databases-Part 1
Speakers: Michael Feldgarden and Arjun Prasad
Audience: Intermediate
In person at Microbe 2023 and recorded

June 19 | Introduction to NGS Public Databases-Part 2
Speakers: Michael Feldgarden and Arjun Prasad
Audience: Intermediate
In person at Microbe 2023 and recorded

June 28 | Assessing Data Quality and Metrics-Part I
Speaker: David Gaston
Audience: Intermediate
Webinar, live and recorded

June 29 | Assessing Data Quality and Metrics-Part II
Speaker: David Gaston
Audience: Intermediate
Webinar, live and recorded

July 2023
July 5 | Molecular Evolution and Community Outbreak
Speaker: Allison Black
Audience: Advanced
Webinar, live and recorded

July 6 | Quality Control Requirements
Speaker: Emily Snavely
Audience: Intermediate
Webinar, live and recorded

July 18 | Assay Design, Optimization and Validation-Part I
Speaker: Trish Simner
Audience: Intermediate
Webinar, live and recorded

July 19 | Assay Design, Optimization and Validation-Part II
Speaker: Trish Simner
Audience: Intermediate
Webinar, live and recorded

July 28 | NGS of Cultured Bacterial and Mycobacterial Pathogens
Speaker: Emily Snavely
Audience: Advanced
Webinar, live and recorded

Funding is provided by the Centers for Disease Control and Prevention. Contract 75D30122c13310​ 

The first 850 individuals who register for each live webinar will be provided login specifics. Note: room capacity is 500. The reason for this is based on earlier events and a much lower attendance than those who registered. It is to accommodate changes in plans, and to ensure those who are available can access the event.  

Webinars will begin promptly at 2:00 p.m. ET. If you are unable to access a room, webinars will be recorded and made available 7 business days after each event.  

Questions? Need assistance? Contact clinmicro@asmusa.org.  

Note: You will be directed to a non-ASM site and required to create a new account to register.

Register