ArticleBioinformatics (Oxford, England)2020
Portable nanopore analytics: are we there yet?
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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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.
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.
Who cites it
15 citing papers in PubMed.
- From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases.Diagnostics (Basel, Switzerland) · 2024Review
- OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- Unlocking the potential of DNA-based tagging: current market solutions and expanding horizons.Nature communications · 2023Article
- HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses.Briefings in bioinformatics · 2023Article
- Coriolis: enabling metagenomic classification on lightweight mobile devices.Bioinformatics (Oxford, England) · 2023Article
- TheFrontiers in microbiology · 2023Article
- Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions.Artificial intelligence in medicine · 2022Article
- AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data.GigaScience · 2022Article
- Precision medicine in mood disorders.PCN reports : psychiatry and clinical neurosciences · 2022Review
- Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions.Quantitative plant biology · 2022Review
- NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data.Computational and structural biotechnology journal · 2022Article
- KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genesFrontiers in bioengineering and biotechnology · 2022Article
- KARGA: Multi-platform Toolkit for... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics · 2021Article
- PHONI: Streamed Matching Statistics with Multi-Genome References.Proceedings. Data Compression Conference · 2021Article
- Sarcoma and the 100,000 Genomes Project: our experience and changes to practice.The journal of pathology. Clinical research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
motivationOxford Nanopore technologies (ONT) add miniaturization and real time to high-throughput sequencing. All available software for ONT data analytics run on cloud/clusters or personal computers. Instead, a linchpin to true portability is software that works on mobile devices of internet connections. Smartphones' and tablets' chipset/memory/operating systems differ from desktop computers, but software can be recompiled. We sought to understand how portable current ONT analysis methods are.
resultsSeveral tools, from base-calling to genome assembly, were ported and benchmarked on an Android smartphone. Out of 23 programs, 11 succeeded. Recompilation failures included lack of standard headers and unsupported instruction sets. Only DSK, BCALM2 and Kraken were able to process files up to 16 GB, with linearly scaling CPU-times. However, peak CPU temperatures were high. In conclusion, the portability scenario is not favorable. Given the fast market growth, attention of developers to ARM chipsets and Android/iOS is warranted, as well as initiatives to implement mobile-specific libraries. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at: https://github.com/marco-oliva/portable-nanopore-analytics.
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What OpenQuestion holds
Registered trials
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 OpenQuestion graph.