Sequencing strategies

Introduction
Whole genome shotgun sequencing
Clone-by-clone sequencing

Whole genome shotgun sequencing

The “rough” assembly of sequences from a genome constitutes a strategy called whole genome shotgun sequencing. This method works well for bacterial genomes, which are small (of the order of several million nucleotides) and do not have many repetitive sequences. The contribution of this strategy to the sequencing of the human genome, which consists of 3 billion nucleotides, half of which are repetitive, remains controversial (see the Human Genome section).

In the case of large genomes, the whole genome shotgun strategy involves obtaining matching sequences at different genomic levels. Thus the ends of large genomic fragments (several hundred thousands of nucleotides) are sequenced, which allows assembly of contigs as large backbones, and permits detection of certain errors within the contigs.