Evidence map›Paper›PMID 41942897›Full record

ArticleBMC genomics2026

Systematic detection of Oxford Nanopore adapter and barcode contamination in GenBank.

Florencia Martino, Abraham J Kandathil, Steven J Clipman

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Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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1 · What the graph read from it

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.

2 · The registry

The trial behind it

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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Florencia MartinoDivision of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0009-0006-1381-6326
Abraham J KandathilDivision of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-9038-134X
Steven J ClipmanDivision of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA. sclipman@jhmi.edu.ORCID http://orcid.org/0000-0002-2366-8420

Funding

Leveraging the plasma virome as a biological indicator of HIV risk and transmission networks among people who inject drugsR01DA058567 · NIDA · JOHNS HOPKINS UNIVERSITY · PI Steven J. Clipman, Abraham Kandathil · 2023 to 2026
$2.7M
Molecular Networks and Deep Learning for Targeted HIV Interventions among PWIDDP2DA056130 · NIDA · JOHNS HOPKINS UNIVERSITY · PI CLIPMAN, STEVEN J. · 2022 to 2022
$2.5M
NIDA NIH HHS DP2 DA056130NIDA NIH HHS L60 DA056996NIDA NIH HHS R01 DA058567NIH HHS DP2DA056130NIH HHS R01DA058567
6 · The paper itself

Abstract

backgroundOxford Nanopore Technologies (ONT) workflows attach synthetic adapters and barcode oligonucleotides to DNA fragments for priming and multiplexing. Although these sequences are normally removed during basecalling or post-processing, incomplete trimming can embed non-biological fragments into genome assemblies deposited in public repositories.

resultsA systematic sequence-similarity screening of the GenBank nucleotide search database identified 5,782 unique accessions containing 13,734 Oxford Nanopore Technologies (ONT) adapter and barcode fragments embedded in bacterial, viral, and eukaryotic assemblies. Most contaminating sequences correspond to rapid-ligation and ligation-based adapters, reflecting incomplete trimming in ONT workflows. Multiple ONT synthetic sequences were often detected within a single accession, consistent with protocols employing several adapters and barcodes. Compared with GC-matched randomized control sequences, the original ONT sequence catalogue yielded significantly more GenBank matches, supporting that the observed signal exceeds chance similarity.

conclusionsThis ONT-specific contamination recurs across GenBank records and exhibits structured patterns across taxonomic groups and project types. Implementing ONT-aware screening during public database submissions and curation is critical to prevent the ongoing propagation of synthetic sequences and safeguard genomic data integrity.

Indexed as

Databases, Nucleic AcidDNA Barcoding, TaxonomicDNA ContaminationNanoporesHigh-Throughput Nucleotide SequencingSequence Analysis, DNAAdapter trimmingBioinformaticsGenome assembliesLong-read sequencingPublic sequence repositoriesQuality controlSequencing artifactsSynthetic oligonucleotides

Identifiers

PMID41942897
PMCPMC13182109

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Registered trials

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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.