All sessions are in Eastern time

Pre-conference Sessions

Sunday, Oct. 16: NCBI Microbial Pathogen and SARS-CoV-2 Resources in the Cloud Workshop—Sold Out!


10 a.m.–3 p.m. (includes a 1-hour break)
Get hands-on experience with NCBI pathogen detection and SARS-CoV-2 surveillance data in the cloud. No prior cloud experience necessary.


  • Cloud computing allows researchers to flexibly use scalable computing for data exploration and analysis and provides a platform that can support FAIR (findable, accessible, interoperable and repeatable) data practices. As part of the NIH’s Science and Technology Research Infrastructure for Discovery, Experimentation and Sustainability (STRIDES) Initiative, NCBI has made sequence, metadata and analysis results available in the cloud for select high-value projects.

Workshop Objectives

  • Learn about available NCBI Pathogen Detection and SARS-CoV-2 Surveillance data on the Google Cloud Platform (GCP). Cloud access will be provided to attendees.
  • Gain practical experience using the GCP Console and BigQuery.
  • Employ methods to search, retrieve and investigate metadata and sequence data and integrate these into your research.
  • Explore SARS-CoV-2 genetic variation and sample metadata and find related sequence data.
  • Learn to use the Pathogen Detection MicroBIGG-E Browser to investigate isolate metadata, genetic and genomic elements (including antimicrobial resistance genes) and find related sequence data.

Target Audience

  • Genomic biologists and bioinformaticians who want to learn more about NCBI cloud-based tools and datasets.


  • A laptop with Wi-Fi access. 
  • Familiarity with command-line. 
For queries or questions, please send an email to

Sunday, Oct. 16: Hackathon Introductory and Planning Session


3:15-4:45 p.m. 
Hackathon: Less Dependency Tracking and More Science Using Bioconda.


  • This session is open to all conference attendees. 


  • Bioconda is a valuable resource that allows the bioinformatics community to do more science and less debugging installs. Additionally, every tool in Bioconda has a Docker container made available from Biocontainers and a Singularity image from the Galaxy Project. 
  • In this session, the hackathon leader will introduce attendees to Bioconda, its many services to the bioinformatics community and details on contributing to Bioconda, including submitting new recipes or reviewing changes. Attendees can expect to leave this session with a better understanding of how they can use Bioconda for their bioinformatic needs and how to make significant contributions to the bioinformatics community.
  • The actual hackathon will be held virtually in fall 2022.


  • Robert Petit, Ph.D., Senior Bioinformatics Scientist, Wyoming Public Health Laboratory

Full Conference Schedule

Sunday, Oct. 16
10 a.m.–3 p.m. 
NCBI Microbial Pathogen and SARS-CoV-2 Resources in the Cloud (Sold Out)

3:15-4:45 p.m. 
Hackathon Introductory and Planning Session: Less Dependency Tracking and More Science Using Bioconda

  • Robert Petit, Ph.D., Senior Bioinformatics Scientist, Wyoming Public Health Laboratory

5–7 p.m.
Opening Session: COVID Origins and Reconstructing the Phylogeny of Those Early SARS-CoV-2 Lineages

  • Michael Worobey, Ph.D., Professor and Department Head of Ecology and Evolutionary Biology, University of Arizona.
  • Jonathan Pekar, M.S., Ph.D. candidate, Department of Biomedical Informatics, University of California San Diego.
The Needle and The Haystack: Sequencing for Pandemic Preparedness and Global Health Equity
  • Nahid Bhadelia, M.D., MALD, Senior Policy Advisor on Global COVID-19 Response, White House COVID-19 Response Team.
7–8:30 p.m.
Opening Reception

Monday, Oct. 17
8:30 a.m.–12 p.m.
Scientific Session 1: Epidemiological Cues: NGS in Clinical and Public Health Microbiology

     8:30–9 a.m.
     Invited Speaker: Daria Van Tyn

     9–10 a.m.
     Epidemiological Cues Oral Abstract Presentations

     10–10:30 a.m.
     Morning Break                   

     12–1:30 p.m. (Lunch will be provided from 12–12:45 p.m.)
     Lunch & Learn: Evaluation of the bioMérieux EPISEQ Software for wgMLST-based Bacterial Strain Typing

     Speaker: Suzane Silbert, Ph.D., Director, Escoteric Testing/R&D and Microbiology Laboratories, Tampa General Hospital
Sponsored by bioMérieux

1:30–5 p.m. 
Scientific Session 2: Bridging Silos: Exploring mechanisms for collecting and sharing microbial genomic data to foster interoperability

     1:30–2 p.m. 
     Invited Speaker: Emiley Eloe-Fadrosh 
     2–3 p.m. 
     Bridging Silos Oral Abstract Presentations

     3–3:30 p.m.
     Afternoon Break

     3:30-5 p.m.
     NCBI-NLM-NIH Joint Panel Discussion: An Institute at the Center of the Next Generation Sequencing Revolution

  • William Klimke—Pathogen Detection: More Than One Million Genomes—Where Do We Go From Here?
  • Ken Katz—SRA NGS Submission, Analysis, and Removing Unintended Human Contamination.
  • J. Rodney Brister –​ SARS-CoV-2 Resources and Analyses, at NCBI Virus and in the Cloud.
5–7 p.m.
     Poster Session #1Poster Board Number Index
     Poster Session #1 Abstracts

Tuesday, Oct. 18
8:30 a.m.–12 p.m.
Scientific Session 3: Secret Ingredient: NGS to Uncover the Role of Microbes in Agricultural and Food Systems

     8:30–9 a.m.
     Invited Speaker: Lawrence Goodridge

     9 a.m.–10 a.m.
     Secret Ingredient Oral Abstract Presentations

     10–10:30 a.m.
     Morning Break                   

     12–1:30 p.m.

1:30–5 p.m. 
Scientific Session 4: Microbial Chatter: Microbial Ecology in Health and Disease

     1:30–2 p.m. 
     Invited Speaker: Jamie Morton

     2–3 p.m. 
     Microbial Chatter Oral Abstract Presentations

     3–3:30 p.m.
     Afternoon Break

     4–5 p.m.
     Microbial Chatter-Wastewater Symposium
     Wastewater Symposium Abstract Oral Presentations 

5–7 p.m.
     Poster Session #2 - Poster Board Number Index
     Poster Session #2 Abstracts

Wednesday, Oct. 19
8:30–12 p.m. 
Scientific Session 5: Pipe Dreams: Analytical Methods, Bioinformatic Tools and Pipelines

     8:30–9 a.m. 
     Invited Speaker: Yatish Turakia

     9–10 a.m. 
     Pipe Dreams Lightning Talk Presentations
     Pipe Dreams Oral Abstract Presentations

     10–10:30 a.m.
     Morning Break 

     10:30 a.m.–12 p.m.
     Scientific Session 5 continues

End of meeting
Download a Certificate of attendance

2022 ASM NGS Conference Session Topics

All sessions will be available for 6 months after the conclusion of the conference.

Epidemiological Cues: NGS in Clinical and Public Health Microbiology

  • Genomic sequencing and molecular epidemiology are indispensable tools for clinical reference diagnostics, public health surveillance outbreak detection and response. This session will discuss how sequencing is being used in clinical and public health microbiology, and the challenges and successes in implementing these technologies successfully in routine and standard practice.

Bridging Silos: Exploring Mechanisms for Collecting and Sharing Microbial Genomic Data to Foster Interoperability

  • Amassing large microbial genomic datasets has become turnkey. However, collecting rich contextual data, getting these datasets submitted to public or private repositories and extracting slices of these data across projects for broader analyses is still a barrier for advancing this field. This session will explore methods for improving contextual data and creating more interoperability between datasets and repositories. 

Secret Ingredient: NGS to Uncover the Role of Microbes in Agricultural and Food Systems

  • Understanding microbial diversity and function in natural and built environments is critical for enhancing productivity, resilience and health of agricultural and food systems. NGS can uncover the role of microbes in soil, plant and animal health. It can also help pinpoint the origins of contamination events, antimicrobial resistance and other pathogen risks. This session will highlight genomic and microbiome research in environmental, veterinary and food microbiology. 

Microbial Chatter: Microbial Ecology in Health and Disease

  • Profiling microbial communities and their functional potential in human and animal hosts is critical to our understanding of host-microbe interactions in health and disease. This session will highlight omics approaches to characterize the microbiome and virome in human and animal studies, as well as novel integrative and interaction network analysis methods. This session will also include studies on pathogen genomics.

Pipe Dreams: Analytical Methods, Bioinformatic Tools and Pipelines ​

  • Recent technology advances have made whole-genome sequencing and other sequencing-based assays ubiquitous in modern microbiology. However, this shift in techniques is generating huge volumes of data that require computational analysis. This session covers new analytical methods and bioinformatics tools designed to surf the growing wave of genomic data.

Program Committee

Ruth Timme – Chair
U.S. Food and Drug Administration
College Park, Md.

Elodie Ghedin—Co-Chair
Bethesda, Md.

Duncan MacCannell
Centers for Disease Control and Prevention
Atlanta, Ga.

George Gthinji
KEMRI/Wellcome Trust Research Programme
Kilifi, Kenya

Torsten Seemann
University of Melbourne
Melbourne, Australia

Sofonias Tessema
Africa CDC
Addis Ababa, Ethiopia

Jasna Kovac
Penn State University

Julie Dunning Hotopp
IGS, University of Maryland, School of Medicine
Baltimore, Md.
Todd Treangen
Rice University
Houston, Texas

Arjun Prasad
NIH, National Center for Biotechnology Information
Bethesda, Md.

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