التفاصيل البيبلوغرافية
| العنوان: |
Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity. |
| المؤلفون: |
Waite, David W., Liefting, Lia, Delmiglio, Catia, Chernyavtseva, Anastasia, Ha, Hye Jeong, Thompson, Jeremy R. |
| المصدر: |
Viruses (1999-4915); Oct2022, Vol. 14 Issue 10, pN.PAG-N.PAG, 23p |
| مصطلحات موضوعية: |
BIOSECURITY, NUCLEOTIDE sequencing, WORKFLOW, RAPID tooling, SEQUENCE analysis, WORKFLOW software, WORKFLOW management systems |
| مستخلص: |
The field of biosecurity has greatly benefited from the widespread adoption of high-throughput sequencing technologies, for its ability to deeply query plant and animal samples for pathogens for which no tests exist. However, the bioinformatics analysis tools designed for rapid analysis of these sequencing datasets are not developed with this application in mind, limiting the ability of diagnosticians to standardise their workflows using published tool kits. We sought to assess previously published bioinformatic tools for their ability to identify plant- and animal-infecting viruses while distinguishing from the host genetic material. We discovered that many of the current generation of virus-detection pipelines are not adequate for this task, being outperformed by more generic classification tools. We created synthetic MinION and HiSeq libraries simulating plant and animal infections of economically important viruses and assessed a series of tools for their suitability for rapid and accurate detection of infection, and further tested the top performing tools against the VIROMOCK Challenge dataset to ensure that our findings were reproducible when compared with international standards. Our work demonstrated that several methods provide sensitive and specific detection of agriculturally important viruses in a timely manner and provides a key piece of ground truthing for method development in this space. [ABSTRACT FROM AUTHOR] |
|
Copyright of Viruses (1999-4915) is the property of MDPI and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) |
| قاعدة البيانات: |
Complementary Index |
Full Text Finder