Assembly Quality Control
One-Sentence Definition
Assembly quality control evaluates whether a reconstructed bacterial genome is complete, uncontaminated, and structurally trustworthy before typing, AMR calling, or phylogenomics.
Simple Explanation
After assembly, ask: is this genome whole, clean, and not a mixed-culture mash — before you trust any resistance or outbreak call.
Detailed Scientific Explanation
| Check | Tools / metrics |
|---|---|
| Contiguity | N50, contig count (QUAST-style reports) |
| Completeness / contamination | CheckM, CheckM2, BUSCO |
| Species consistency | ANI and Species Delineation, GTDB-Tk |
| Mixed cultures | Multiple MLST alleles, abnormal GC bimodality (Contaminant and Mixed-Culture Detection) |
| Gene content sanity | Unexpected plasmid/AMR from contaminants |
Thresholds used in many pipelines: near-complete (≥95–97% completeness), low contamination (≤5%), reasonable contig counts for the sequencer used.
Long-read / hybrid assemblies change expectations (fewer contigs, closed chromosomes/plasmids) — see Long-Read and Hybrid Bacterial Assembly.
Mechanism
Compute marker-gene presence and gene redundancy → estimate completeness/contamination → combine with assembly graph statistics → pass/fail for downstream WGS Bioinformatics Pipeline.
Clinical Importance
- Prevents false outbreak links and false AMR genes from contaminated assemblies.
- Accreditation-minded labs document QC gates before reporting WGS results.
Research Importance
- Essential for public database submissions and meta-analyses.
Diagnostic Relevance
- Hard gate in clinical WGS SOPs; fail → resequence or restrict interpretation.
AMR Relevance
Contaminant DNA can inject spurious resistance genes into reports — dangerous for stewardship (AMR Gene Databases).
Related Methods
Related MOCs
Active Recall Questions
- What do CheckM completeness and contamination estimate?
- Why can a high N50 still be a bad assembly for clinical use?
- Name a red flag for mixed-culture assemblies.