Evidence map›Paper›PMID 40417475›Full record

ArticleAMIA ... Annual Symposium proceedings. AMIA Symposium2024

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

Simone Marini, Alexander Barquero, Anisha Ashok Wadhwani, Jiang Bian, Jaime Ruiz, Christina Boucher, Mattia Prosperi

Abstract read
PubMed Full text at PMC
In one paragraph

Article in AMIA ... Annual Symposium proceedings. AMIA Symposium, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Simone MariniDepartment of Epidemiology, University of Florida, Gainesville, USA.
Alexander BarqueroDepartment of Computer and Information Science and Engineering, University of Florida, USA.
Anisha Ashok WadhwaniDepartment of Computer and Information Science and Engineering, University of Florida, USA.
Jiang BianDepartment of Health Outcomes and Biomedical Informatics, University of Florida, USA.
Jaime RuizDepartment of Computer and Information Science and Engineering, University of Florida, USA.
Christina BoucherDepartment of Computer and Information Science and Engineering, University of Florida, USA.
Mattia ProsperiDepartment of Epidemiology, University of Florida, Gainesville, USA.

Funding

A Phylodynamic Artificial Intelligence framework to predict evolution of SARS-CoV-2 variants of concern in Immunocompromised persons with HIV (PhAI-CoV)R01AI170187 · NIAID · UNIVERSITY OF FLORIDA · PI MARIA LUISA ALCAIDE, Deborah Lynne Jones · 2022 to 2026
$3.7M
Forecasting trajectories of HIV transmission networks with a novel phylodynamic and deep learning frameworkR01AI145552 · NIAID · UNIVERSITY OF FLORIDA · PI Simone Marini, Mattia Prosperi · 2020 to 2026
$3.6M
Developing Computational Methods for Surveillance of Antimicrobial Resistant AgentsR01AI141810 · NIAID · UNIVERSITY OF FLORIDA · PI BOUCHER, CHRISTINA, PROSPERI, MATTIA · 2019 to 2023
$2.1M
NIAID NIH HHS R01 AI141810NIAID NIH HHS R01 AI145552NIAID NIH HHS R01 AI170187
6 · The paper itself

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.

Indexed as

MetagenomicsMobile ApplicationsSoftware

Identifiers

PMID40417475
PMCPMC12099329

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.