2026 Midwest Bioinformatics Training #

May 12-13, 2026 ~ Michigan Department of Health & Human Services, Bureau of Laboratories ~ Lansing, MI

About: The 2026 Midwest Bioinformatics Training provided beginner-level, hands-on experience running basic bioinformatics pipelines using a command line interface (CLI) to process raw sequencing reads, produce high-quality assembled genomes using two different assembly methods, and perform downstream analyses. Along with first-hand experience running bioinformatics pipelines, participants gained an understanding of the purpose and importance of each step within the workflow. Key concepts included sequence quality interpretation, genome assembly, phylogenetic analysis, and implementing best practices for bioinformatics pipelines in public health.

Training Participation: A total of 27 trainees from 14 State & Local public health jurisdictions including laboratorians (55%), genomic epidemiologists (30%), and other AMD-related roles (15%) participated in this training.

Training Coordinators - MDHHS #

• Macy Pell, PhD - AMD Training Lead
• Madison Walton-Franklin, PhD - Genomic Epidemiology Training Lead
• Arianna Miles-Jay, PhD, MPH - Genomic Analysis Unit Manager
• Heather Blankenship, PhD - Genomics Technical Director

  Training Developers - MDHHS #

• John Chodkowski, PhD - Bioinformatics Specialist
• Douglas Maldonado-Torres, MS - Bioinformatician
• Karla Vasco, DVM, MSc, PhD - Bioinformatics Specialist

Training Content #

1. Overview of bioinformatics in public health #

• History of bioinformatics in public health
• Technical overview of bioinformatics pipelines
• Intro to GitHub Codespaces platform

2. Training Module 1: Getting to know the pipeline #

• Assessing read quality with FastQC
• Read processing with fastp
• Activity: Interpreting sequence quality
• Genome assembly methods overview
• Performing de novo genome assembly
• Assessing assembly quality with QUAST and MultiQC

3. Training Module 2: End-to-end pipeline & reference-based assembly #

• End-to-end pipelines
• Reference-based genome assembly
• Activity: Interpreting assembly quality

4. Training Module 3: Bacterial whole genome sequencing analysis #

• Beyond assembly: comparing pathogen sequences to gain public health insights
• MLST typing
• Variant calling with Snippy
• Core SNP alignment with Snippy-core
• Constructing a phylogenetic tree with IQtree
• Visualizing phylogenetic trees using Microreact
• Genome annotation with Prokka
• Pangenome analysis with Panaroo & visualization

5. Tools, tips, and tricks: Q&A panel with bioinformatics experts #

6. Best practices: Introduction to Nextflow #

Resources #

• Revisit the training modules and keep practicing -> MDHHS-Bioinformatics-Training GitHub organization
• Agenda
• View and download photos from the training

Funding acknowledgement #

This training event was made possible through funding provided under the Epidemiology and Laboratory Capacity (ELC) for Prevention and Control of Emerging Infectious Diseases Cooperative Agreement (CK24-0002), Project D: Advanced Molecular Detection to the Michigan Department of Health & Human Services. The conclusions, findings, and opinions expressed by presenters and organizers of this event do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Services, or the Centers for Disease Control and Prevention.