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

Genes
Samir V DeshpandeMary M Wade

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 Nano...Continue Reading

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Citations

Mar 22, 2020·Scientific Reports·Robert Maximilian LeidenfrostRöbbe Wünschiers
Feb 20, 2020·Computational and Structural Biotechnology Journal·Andres SantosJaime Martinez-Urtaza
Jan 15, 2021·FEMS Microbiology Ecology·Lee J Kerkhof
Jun 15, 2021·EcoSal Plus·Eric W BrownMarc W Allard

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Methods Mentioned

BETA
PCR

Software Mentioned

MinIT
Pan
Ubiq
WIMP
Centrifuge
MinION
ONT
Genomics for Infectious Agents ( PanGIA )
Empowering the Development of Genomics Expertise ( EDGE )
Windows

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