Today there exists a multitude of different genome sequencing techniques, and distinct complexities are associated with each method. However, the number of pair

Today there exists a multitude of different genome sequencing techniques, and distinct complexities are associated with each method. However, the number of pairs is today seldomly the main complexity. Sanger sequencing was one of the first methods of sequencing, and employs linear sequencing: the synthesis of strands with increasing length. With the advent of the Human Genome Project, Celera instead came up with the idea of fragmenting the genome, amplifying the fragments, sequence the fragments, and match them together using bioinformatics. The complexity here lies in that much of the DNA is repeated (such as microsatellites) or no, which makes it hard to 'phase' the genome. As such, a short 20 nucleotide sequence may be present in may parts of the genome which makes it hard to generate a 100% complete connected genome. Today, Illumina sequencing is the major sequencing platform (~85% of market share). It relies of the fragmentation of DNA into ~300 bp fragments. By synthesising the complementary strand of each fragment with fluorescent nucleotides, we may employ lasers to detect (sequence) the nucleotides of the fragments. Here we have the same problem as with shotgun sequencing: that we have many repeats in the DNA sequence. To remedy this, error-prone sequencing methods with long read lengths such as IonTorrent/PacBio/etc. may be employed to. These long reads may then act as a map for stiching together the more precise short reads. This is called 'hybrid' sequencing. Other sequencing methods, such as Pyrosequencing, has the inherent problem of not being able to discern too many (5) of the same nucleotide in a row. Other methods are primer based (i.e. need to know a short subsequence of the DNA beforehand). This is problematic if we want to perform a de-novo whole genome sequence. Note: Illumina does not rely on primers, and may be deployed directly on unknown sequences, unlike Pyrosequencing/Sanger sequencing.