Table 1.
Alignment Strategies for Different Types of Assemblies
| Method | Scheme of alignment | Examples |
| Contigs | Individual contigs | Finished BACs |
| Scaffold | Contigs can be reoriented and reordered | Arachne October 2001 Phusion November 2001 |
| Chopped pieces | Mouse chromosomes are chopped in 250 kb and aligned to the Human Genome | Celera chromosome 16 MGSC v3 |
