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

Abstract

Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in 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. Here 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, and yielding high correlation on real-word data. OCTOPUS is available along with customized databases at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.

Figure 1.

Calculation of k-mer minimizers using rolling hash (A), k-mer probabilistic filtering based on species’ cooccurrence (B), and compact (64- to 32-bit) k-mer indexing through Bloom filters, minimal perfect hashing and compression (C).

Figure 2.

Comparison of classification performance between OCTOPUS and Kraken2. Panel (A) and (B) show the distribution of sensitivity and precision on simulated bacterial datasets (4,202 genomes, ~10 million reads), while panel (C) shows the false positive rate on non-bacterial datasets made of mammalian and viral genomes (7 genomes and 241,673 reads, 47 genomes and 3,621 reads, respectively).