Microbiology Encyclopedia

WGS Bioinformatics Pipeline

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WGS Bioinformatics Pipeline

One-Sentence Definition

A WGS bioinformatics pipeline is the ordered set of computational steps that converts raw sequencing reads into annotated genomes, typing results, and AMR/virulence reports.

Simple Explanation

DNA sequencer → computer recipe → “species + resistance genes + family tree.”

Detailed Scientific Explanation

Typical isolate pipeline:

  1. QC / trim — Read QC and Preprocessing
  2. Contamination check — mixed samples fail downstream
  3. Assembly or reference mapping — Genome Assembly · Variant Calling in Bacteria
  4. Species / strain ID — ANI (Comparative Genomics), mash, MLST and cgMLST
  5. Annotation — Genome Annotation
  6. AMR / virulence — AMR Gene Databases · Virulence Factor Databases
  7. Plasmid / mobile element calls — Plasmid and Mobile Element Analysis
  8. Phylogeny — Phylogenomics and Outbreak Typing · Phylogenetic Tree Building
  9. Report — clinical/epi narrative + versions of DBs/tools (Reproducible Bioinformatics Workflows)

Long-read or hybrid adds structural accuracy for plasmids (Sequencing Technologies).
Commands for each step: Genomics Command-Line Cheatsheet.

Mechanism

Each step transforms file types (FASTQ→BAM/FASTA→GFF/JSON reports). Reproducibility requires containerized tools + pinned DB versions.

Clinical Importance

  • Turnaround and validation define whether WGS is epi-only or patient-facing
  • Wrong pipeline version → inconsistent outbreak calls

Research Importance

  • Benchmarking assemblers; plasmid graphs; FAIR sharing

Diagnostic Relevance

AMR Relevance

Active Recall Questions

  1. Why pin database versions in clinical pipelines?
  2. Which step catches a mixed isolate early?
  3. Why might plasmids need long reads?

Connections

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