Management and analysis of high-throughput sequence data for animal infectious disease

27/10/2022

R.J. Ellis & T.L. Jenkins

Advances in technology and decreasing costs have accelerated the use of high-throughput sequencing (HTS) for both diagnosis and characterisation of animal infectious disease. HTS offers advantages over previous techniques, such as rapid turnaround times and the ability to resolve single nucleotide changes among samples, both of which are important for supporting epidemiological investigations of outbreaks. However, due to the plethora of genetic data being routinely generated, this has introduced challenges associated with the storage and analysis of these data. This article provides insight into the areas of data management and analysis that should be considered prior to adopting HTS for routine animal health diagnostics, which fall largely into three interrelated categories: data storage, data analysis and quality assurance. There are numerous complexities in each and they may need to be adapted as HTS evolves. Making appropriate strategic decisions regarding bioinformatic sequence analysis early on in project development will avert major issues in the long term.

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