Advancing Data Strategies for Tracking Infectious Diseases

Kelsey Florek, PhD, MPH
Senior Genomics and Data Scientist
Wisconsin State Laboratory of Hygiene
June 6, 2024

Slides live at:

Next Generation Sequencing for Infectious Disease Surveillance

What is Next Generation Sequencing?

Sanger Sequencing

Next Generation Sequencing (Illumina)

High-throughput requires advanced analytics (Nextseq 2000)

  • 30,000,000,000 ATGC's generated per sequencing run
  • 40,000 - 150,000 words in a novel
  • average word length in English is 4.79
  • one sequencing run would generate 62,000 novels with 100,000 words each

Anatomy of a Bioinformatics Workflow

              include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'

              workflow INPUT_CHECK {
                  samplesheet // file: /path/to/samplesheet.csv
                  SAMPLESHEET_CHECK ( samplesheet )
                      .splitCsv ( header:true, sep:',' )
                      .map { create_fasta_channel(it) }
                      .set { reads }
                  // channel: [ val(meta), [ path_to_reads ] ]
                  // channel: [ samplesheet.valid.csv ]                   
                  csv = SAMPLESHEET_CHECK.out.csv
                  // channel: [ versions.yml ]
                  versions = SAMPLESHEET_CHECK.out.versions 
              // Function to get list of [ meta, [ fasta ] ]
              def create_fasta_channel(LinkedHashMap row) {
                  // create meta map
                  def meta = [:]
                     = row.sample
                  def fasta_meta = []
                  if (!file(row.fasta).exists()) {
                      exit 1
                  } else {
                      fasta_meta = [ meta, [ file(row.fasta) ] ]
                  return fasta_meta

Sequencing Reads

              @M05192:295:000000000-K6N36:1:1101:9502:1212 1:N:0:NAGCGCTC+NCGTAAGA
              @M05192:295:000000000-K6N36:1:1101:13064:1213 1:N:0:NAGCGCTC+NCGTAAGA
              @M05192:295:000000000-K6N36:1:1101:18301:1216 1:N:0:NAGCGCTC+NCGTAAGA
              @M05192:295:000000000-K6N36:1:1102:8809:23354 1:N:0:TAGCGCTC+GCGTAAGA
              @M05192:295:000000000-K6N36:1:1102:12222:23342 1:N:0:TAGCGCTC+GCGTAAGA
              @M05192:295:000000000-K6N36:1:1102:17996:23344 1:N:0:TAGCGCTC+GCGTAAGA

Phylogenetic Tree

WSLH CDD Bioinformatic Workflows

  • Spriggan
  • AR Report Generator
  • SPNTypeID

Public Health Application of
Infectious Disease Genomics

  • Pathogen Surveillance
    • trends
    • prioritization and risk assessment
    • early warning system
  • Outbreak Response
    • source tracking
    • containment
    • risk assessment

Application of Genomic Data to Outbreaks

Application of Genomic Data to Surveillance

SARS-CoV-2 Variant Waves in WI

SARS-CoV-2 Variant Waves in WI

Pathogen Surveillance: SARS-CoV-2

SARS-CoV-2 Wastewater

SARS-CoV-2 Clinical

Advancing Genomics in the Cloud

What is the cloud?

Cloud Data Strategies

Genomic Data Lake

Genomic Data Cloud Infrastructure

Monitoring Data Workflows with Nextflow Tower

Monitoring Data Workflows with Nextflow Tower

WSLH Data Portal Infrastructure

AWS Glue and MapReduce

  • Map: input data is first split into smaller blocks, then each block is assigned to a separate worker node and processed in parallel
  • Shuffle: worker nodes redistribute data such that all data belonging to a group located on the same worker node
  • Reduce: if needed worker nodes then process each group of output data, in parallel

AWS Glue and MapReduce

Query Data in the Data Lake

Simplifying Genomics for Public Health Partners

AMD Bioinformatics Regional Resource - Midwest Region

Ad-hoc Analytical Support

Provision of Computational Resources

Easy Genomics Partnership

Easy Genomics - Minimal Viable Product

  • Simplify the process of launching and monitoring workflows
  • Provide the ability for users to upload sequence data through the web browser
  • Allow users to download analysis results through the web browser
  • User/Lab separation

Easy Genomics - Sequence Data Upload

Easy Genomics - Launch

Easy Genomics - Launch

Easy Genomics - Monitor

Easy Genomics - Monitor

Easy Genomics - Roadmap

  • 2024 Spring - Deploy Easy Genomics for internal use
  • 2024 Early Summer - Open Access to SARS-CoV-2 Sequencing Laboratories
  • 2024 Mid Summer - Easy Genomics MVP Update
  • 2025 Winter - Deploy Easy Genomics in CDC National Bioinformatics Platform


Abigail Shockey, PhD
Christopher Jossart, MPH
Dustin Lyfoung, MS
Thomas Blader
Eva Gunawan, MS

Special Thanks