Genome Assembly
One-Sentence Definition
Genome assembly reconstructs contiguous DNA sequences (contigs/scaffolds/complete chromosomes) from overlapping sequencing reads.
Simple Explanation
Reads are puzzle pieces; assembly puts the microbial genome picture together.
Detailed Scientific Explanation
- De novo (SPAdes, Unicycler) vs reference-guided mapping
- Short reads: high accuracy bases, fragmented plasmids/repeats
- Long reads (ONT/PacBio): better continuity, need polishing
- Hybrid assembly: best of both for many bacterial genomes
- Metrics: N50, completeness (CheckM), contamination
Mechanism
Graph of overlaps (de Bruijn / overlap graphs) → path through graph → contigs; unresolved repeats create breaks — common at rRNA and insertion sequences.
Clinical Importance
- Incomplete plasmid assembly → missed carbapenemase context
- Mis-assembly can create false gene fusions (rare but important QC)
Research Importance
- Closed genomes for reference; mobile element architecture
Diagnostic Relevance
- Core step in WGS Bioinformatics Pipeline / Whole-Genome Sequencing
AMR Relevance
- Plasmid-borne AMR needs correct graph resolution — link Plasmid · Conjugation
Related MOCs
Active Recall Questions
- Short-read vs long-read tradeoff?
- What genomic features break assemblies?
- Why does plasmid closure matter for CRE epi?