Sequence Finishing on New Platforms

Abstract

In the past five years, next generation sequencing (NGS) technology platforms have been released and have become the tool of choice for sequencing genomes. Methods for sequence finishing have had to be updated to deal with the issues created by NGS platforms. Finishing begins with the assembling of the reads produced by the sequencing machines before computational gap closure is attempted. Remaining gaps are identified and suitable experimental techniques such as polymerase chain reactions are used to close these. Until recently, the aim for many genome sequencing projects has been to fully finish genomes. However, due to the time and cost associated with finishing, the majority of future genomes will only reach a high‐quality draft. New genome standards have had to be defined to better reflect the types of sequencing now being undertaken. Improvements to the current generation of sequencing machines along with the advent of the third‐generation technologies means that new ways of dealing with the data volume will need to be sought.

Key Concepts:

  • Next generation sequencing platforms have generated new issues for sequence finishing, which have required novel solutions.

  • Genome standards have had to be updated to better reflect NGS data.

Keywords: next generation sequencing; finishing; Roche (R) 454 Life Science Genome Sequencer; Illumina (R) Genome Analyzer II; Applied Bioystems (R) SOLiD system; DNA; PCR

Figure 1.

Portion of a gap4 window showing 454 reads with differing numbers of base calls in a homopolymer run. The correct sequence is shown in red (Illumina consensus).

Figure 2.

(a) Gap5 visualisation window showing all Illumina reads present compared to (b) a gap4 window showing only an Illumina consensus (subset_4800000).

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Web Links

Illumina website: www.illumina.com

Life/APG SOLiD 3: http://www.appliedbiosystems.com/

Roche 454 Website: www.454.com

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How to Cite close
van Tonder, Andries J, and Grafham, Darren(Mar 2011) Sequence Finishing on New Platforms. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023157]