Despite the multiple coverage, sometimes certain genomic regions remain unsequenced, mainly owing to cloning difficulties.

Genome mapping, assembly, and comparison are related processes:
 

Genome mapping: A physical map is created using DNA fragments and markers to assemble larger DNA sections. DNA base locations can be identified from the overlapping sections of the fragments.
Genome assembly: The process of putting nucleotide sequences into the correct order.
Genome comparison: A comparison of general features of genomes, such as genome size, number of genes, and chromosome number
 

Topics include: Genome Mapping, Genome Sequencing, Genome Sequence Assembly, Genome Annotation, & Comparative Genomics.