Bioinformatics Aspects of High-Throughput Sequencing Technology
Dan MacLean and David J. Studholme
from: Plant Pathogenic Bacteria: Genomics and Molecular Biology (Edited by: Robert W. Jackson). Caister Academic Press, U.K. (2009)
Recently developed massively high throughput sequencing technologies look set to revolutionise the way that we practise research in microbial and plant sciences, and will necessitate greater investment in data management and analysis than in the past. In this manuscript, we describe some of the informatics issues and solutions that we have come across in the early stages of using these new technologies both for resequencing and de novo sequencing. As well as issues directly connected with the infrastructure and technology of high throughput sequencing, we present a brief tour of many more traditional sequence analysis tools that will continue to be relevant in the context of larger datasets.