Sequence Finishing

Abstract Sequence finishing can be described as the manual enhancement of assembled shotgun sequence data to improve regions of low quality or close gaps in the sequence. Shotgun sequencing data can be whole genome derived or from clone‐based entities such as bacterial artificial chromosomes (BACs) or other plasmid based vectors such as fosmids. Sequence finishing can be achieved using a combination of laboratory and computational techniques to produce a highly accurate and complete deoxyribonucleic acid (DNA) sequence. Variable coverage and sequence gaps can occur across whole genome shotgun or a particular BAC or fosmid owing to the random nature of shotgun sequencing and the composition of a given piece of DNA can be prohibitive to both the cloning and sequencing process. A targeted approach is required to provide a more cost effective means of improving any regions of low quality and to close gaps that remain after initial shotgun sequencing. Key Concepts: Gaps exist in shotgun sequence for various reasons including structural elements, which can interrupt the sequencing reaction and variation in coverage owing to chance. Directed finishing to close gaps in shotgun DNA sequence is labour intensive compared with high throughput shotgun sequence generation. Good quality complete DNA sequences facilitate genome annotation and comparative sequencing studies.