Table 1.

Main limitations of short-read next-generation sequencing (NGS) which may be overcome by long-read sequencing.

DNA structure	Why short-read NGS misses it
Structural variants (SVs)	Structural variants such as insertions, deletions, or inversions larger than 1 kilo-base (Kb) pair cannot be detected [76% improved detection of SVs with LRS when compared with short-read NGS (5, 6)]
Copy number variants (CNVs)	Genetic traits involving the number of copies of a particular gene present in the genome of an individual are mostly undetectable
Widespread repeats	Repetitive sequences are poorly or not detected
Segmental duplications	Sequences with numerous homologous elements are poorly or not detected