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Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data

Agricultural high throughput diagnostics need to be fast, accurate and have multiplexing capacity. Metagenomic sequencing is being widely evaluated for plant and animal diagnostics. Bioinformatic analysis of metagenomic sequence data has been a bottleneck for diagnostic analysis due to the size of t...

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Autores principales: Espindola, Andres S., Cardwell, Kitty F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7912148/
https://www.ncbi.nlm.nih.gov/pubmed/33525397
http://dx.doi.org/10.3390/plants10020250
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author Espindola, Andres S.
Cardwell, Kitty F.
author_facet Espindola, Andres S.
Cardwell, Kitty F.
author_sort Espindola, Andres S.
collection PubMed
description Agricultural high throughput diagnostics need to be fast, accurate and have multiplexing capacity. Metagenomic sequencing is being widely evaluated for plant and animal diagnostics. Bioinformatic analysis of metagenomic sequence data has been a bottleneck for diagnostic analysis due to the size of the data files. Most available tools for analyzing high-throughput sequencing (HTS) data require that the user have computer coding skills and access to high-performance computing. To overcome constraints to most sequencing-based diagnostic pipelines today, we have developed Microbe Finder (MiFi(®)). MiFi(®) is a web application for quick detection and identification of known pathogen species/strains in raw, unassembled HTS metagenomic data. HTS-based diagnostic tools developed through MiFi(®) must pass rigorous validation, which is outlined in this manuscript. MiFi(®) allows researchers to collaborate in the development and validation of HTS-based diagnostic assays using MiProbe™, a platform used for developing pathogen-specific e-probes. Validated e-probes are made available to diagnosticians through MiDetect™. Here we describe the e-probe development, curation and validation process of MiFi(®) using grapevine pathogens as a model system. MiFi(®) can be used with any pathosystem and HTS platform after e-probes have been validated.
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spelling pubmed-79121482021-02-28 Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data Espindola, Andres S. Cardwell, Kitty F. Plants (Basel) Article Agricultural high throughput diagnostics need to be fast, accurate and have multiplexing capacity. Metagenomic sequencing is being widely evaluated for plant and animal diagnostics. Bioinformatic analysis of metagenomic sequence data has been a bottleneck for diagnostic analysis due to the size of the data files. Most available tools for analyzing high-throughput sequencing (HTS) data require that the user have computer coding skills and access to high-performance computing. To overcome constraints to most sequencing-based diagnostic pipelines today, we have developed Microbe Finder (MiFi(®)). MiFi(®) is a web application for quick detection and identification of known pathogen species/strains in raw, unassembled HTS metagenomic data. HTS-based diagnostic tools developed through MiFi(®) must pass rigorous validation, which is outlined in this manuscript. MiFi(®) allows researchers to collaborate in the development and validation of HTS-based diagnostic assays using MiProbe™, a platform used for developing pathogen-specific e-probes. Validated e-probes are made available to diagnosticians through MiDetect™. Here we describe the e-probe development, curation and validation process of MiFi(®) using grapevine pathogens as a model system. MiFi(®) can be used with any pathosystem and HTS platform after e-probes have been validated. MDPI 2021-01-28 /pmc/articles/PMC7912148/ /pubmed/33525397 http://dx.doi.org/10.3390/plants10020250 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Espindola, Andres S.
Cardwell, Kitty F.
Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data
title Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data
title_full Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data
title_fullStr Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data
title_full_unstemmed Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data
title_short Microbe Finder (MiFi(®)): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data
title_sort microbe finder (mifi(®)): implementation of an interactive pathogen detection tool in metagenomic sequence data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7912148/
https://www.ncbi.nlm.nih.gov/pubmed/33525397
http://dx.doi.org/10.3390/plants10020250
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