OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.
bioRxiv
; 2024 Aug 10.
Article
en En
| MEDLINE
| ID: mdl-38559026
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 .
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Contexto en salud:
2_ODS3
Problema de salud:
2_cobertura_universal
Idioma:
En
Revista:
BioRxiv
Año:
2024
Tipo del documento:
Article