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

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.

Flesh ID: Nanopore Sequencing Combined with Offline BLAST Search for the Identification of Meat Source

“…Oxford nanopore offers a range of online data analyzing tools. Sequencing data can be uploaded to the cloud-based Epi2Me platform for real-time analysis workflows [ 22 ]. Unfortunately, only virus, bacteria, fungi, and archaea sequences can be recognized by Epi2Me .…”

Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?

“…The software was designed for users without a scientific education or laboratory background, with a focus on detection and enumeration (Deshpande et al . 2019 ).…”

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

“…Individual OTUs are compared against a reference database. Many pipelines, such as MINDS [76] or WIMP [77] are based on the taxonomic classification tool Centrifuge [78].…”