OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier

Presentation Time: 02:15 PM - 02:30 PM

Abstract Keywords: Bioinformatics, Mobile Health, Computational Biology, Omics (genomics, metabolomics, proteomics, transcriptomics, etc.) and Integrative Analyses
Primary Track: Foundations
Programmatic Theme: Public Health Informatics

Portable genomic sequencers such as Oxford Nanopore’s MinION enable real-time applications in both clinical and environmental health. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. In this work, we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases, making it ideal for running on smartphones or tablets. OCTOPUS obtains sensitivity and precision comparable to Kraken2, while dramatically decreasing (4- to 16-fold) the false positive rate. OCTOPUS is available along with customized databases at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.

Speaker(s):
Simone Marini, PhD
University of Florida

Author(s):
Simone Marini, PhD - University of Florida; Alexander Barquero, Mr - University of Florida; Anisha Ashok Wadhwani, MSc - University of Florida; Jiang Bian, PhD - University of Florida; Jamie Ruitz, PhD - University of Florida; Christina Boucher, PhD - University of Florida; Mattia Prosperi, PhD, FAMIA - University of Florida;