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A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field
Open AccessCommunication

Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)

1
Science and Technology Corporation, 111 Bata Blvd, Suite C, Belcamp, MD 21017, USA
2
US Army, 20th CBRNE, Aberdeen Proving Ground, MD 21010, USA
3
US Army, CCDC—Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA
4
Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd, New Brunswick, NJ 08901-8521, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(8), 578; https://doi.org/10.3390/genes10080578
Received: 3 July 2019 / Revised: 25 July 2019 / Accepted: 25 July 2019 / Published: 30 July 2019
(This article belongs to the Special Issue MetaGenomics Sequencing In Situ)
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Abstract

Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies’ (ONT) cloud-based What’s In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT’s framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC’s 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT’s MinION portability, ease-of-use, and identification capability in remote locations. View Full-Text
Keywords: phylogenetic classification; visualization; third generation sequencing; offline analysis pipeline phylogenetic classification; visualization; third generation sequencing; offline analysis pipeline
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Deshpande, S.V.; Reed, T.M.; Sullivan, R.F.; Kerkhof, L.J.; Beigel, K.M.; Wade, M.M. Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS). Genes 2019, 10, 578.

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