• Error rate. The error rate of modern short-read sequencing technologies is smaller than that of modern long-read technologies.

• Genome coverage. Throughput (i.e., the number of reads) of modern short-read sequencing technologies is higher than that of modern long-read technologies.

• Global position. Determine a global position of the read by identifying the starting position or positions of the reads in the reference genome. This step is ambiguous with short reads, as the repetitive structure of the human genome causes such reads to align to multiple locations of the genome. In contrast, long reads are usually longer than the majority of repeat regions and are aligned to a single location in the genome.

• Local pairwise alignment. After determining the global position of each read, the algorithms map all bases of the read to the reference segments, located at these global positions, in order to account for indels. Due to the smaller error rate of short-read technologies, it is usually easier to perform local alignment on short reads than on long ones.

• Genomic variants. Single-nucleotide polymorphisms (SNPs) are easy to detect using short reads when compared to long reads due to the lower error rate and higher coverage of short-read sequencing technologies. Structural variants (SVs) are easy to detect with long reads, which span the entire SV region. Current long-read-based tools [184] are able to detect deletions and insertions with high precision. The sparse coverage of long reads may lower the sensitivity of detection.