Genome Assembly and Advanced NGS
Pitfalls
- k-mer size is critical: Too small → ambiguous graph, unresolvable repeats. Too large → breaks at sequencing errors. Practical: k=31–127 for Illumina; SPAdes uses multiple k simultaneously.
- OLC is O(n²) — not for short reads: Pairwise overlap computation is prohibitive for billions of Illumina reads. Use de Bruijn graph for short reads.
- Repeat content breaks assemblies: Repeats longer than read length create irresolvable branches.
[Description truncada. Veja o README completo no GitHub.]