Figure - WGS Bioinformatics Pipeline

Purpose

Memorize the isolate WGS analysis order from FASTQ to report.

Used In

• WGS Bioinformatics Pipeline
• MOC - Bioinformatics in Microbiology
• Whole-Genome Sequencing
• Learning Media Hub

Diagram

flowchart LR
  A[FASTQ reads] --> B[QC / trim]
  B --> C[[Genome Assembly]]
  C --> D[Species / MLST]
  D --> E[Annotation]
  E --> F[[AMR Gene Databases]]
  E --> G[Virulence genes]
  C --> H[[Phylogenomics and Outbreak Typing]]
  F --> I[Versioned report]
  H --> I
  I --> J{Need MIC?}
  J -->|therapy| K[[Antimicrobial Susceptibility Testing]]

Teaching Legend

Step	Failure mode
QC	Bad library → garbage assembly
Assembly	Broken plasmids → missed AMR context
AMR DB	Wrong version → discordant calls
Phylogeny	Ignoring epi → false outbreak

Quick Self-Check

1. Where does CARD/ResFinder run in this flow?
2. Why is AST still on the chart?