Evidence map›Paper›PMID 41686650›Full record

ArticleBriefings in bioinformatics2026

NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.

Chia-Chen Chu, Jhong-He Yu, Shang-Che Kuo, Fan-Wei Yang, Chia-Chang Lin, Chang-Hung Chen, Yi-Chen Wu, Cing Shih, Ying-Hsuan Sun, Te-Lun Mai and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

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

0numbers the graph read from it
0cells of the map it votes in
0citing 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

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

14 authors.

Chia-Chen ChuDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.ORCID 0000-0003-3026-9206
Jhong-He YuDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.
Shang-Che KuoDepartment of Pharmacy, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St. Beitou Dist., Taipei 11221, Taiwan.ORCID 0000-0002-6773-8179
Fan-Wei YangDepartment of Pharmacy, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St. Beitou Dist., Taipei 11221, Taiwan.
Chia-Chang LinDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.
Chang-Hung ChenDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.
Yi-Chen WuDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.
Cing ShihDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.
Ying-Hsuan SunDepartment of Forestry, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung 40227, Taiwan.
Te-Lun MaiDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.ORCID 0000-0002-9356-6198
Ying-Lan ChenDepartment of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No. 1, University Rd., East Dist., Tainan 70101, Taiwan.ORCID 0000-0003-3145-7882
Hsin-Hung LinDepartment of Agronomy, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung 40227, Taiwan.
Jung-Chen SuDepartment of Pharmacy, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St. Beitou Dist., Taipei 11221, Taiwan.ORCID 0000-0002-8005-0897
Ying-Chung Jimmy LinDepartment of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.ORCID 0000-0001-7120-4690

Funding

Ministry of Science and Technology of Taiwan 109-2636-B-002-003Ministry of Science and Technology of Taiwan 109-2636-B-006-009Ministry of Science and Technology of Taiwan 109-2636-B-010-008Ministry of Science and Technology of Taiwan 110-2628-B-002-026Ministry of Science and Technology of Taiwan 110-2636-B-006-008Ministry of Science and Technology of Taiwan 110-2636-B-A49A-502Ministry of Science and Technology of Taiwan 111-2628-B-002-020Ministry of Science and Technology of Taiwan 111-2636-B-006-015Taiwan National Science and Technology Council 111-2628-B-A49-010Taiwan National Science and Technology Council 112-2311-B-002-023-MY3Taiwan National Science and Technology Council 112-2320-B-A49-023Taiwan National Science and Technology Council 112-2636-B-006-006Taiwan National Science and Technology Council 113-2628-B-002-023Taiwan National Science and Technology Council 113-2636-B-006-004Taiwan National Science and Technology Council 114-2628-B-002-008Yen Tjing Ling Medical Foundation CI-113-3Yen Tjing Ling Medical Foundation CI-114-14
6 · The paper itself

Abstract

NanoPrePro is a streamlined read preprocessor specifically designed for high precision in identifying full-length reads from Oxford Nanopore Technology (ONT) transcriptomic sequencing results, achieved through the precise identification of adapters/primers. However, the preprocessing of ONT reads has been a long-term neglected and ambiguous area without thorough and systematic investigation. Here, we developed NanoPrePro that outperformed the current best preprocessor, Pychopper, using simulated and real datasets. Through sequence similarity, adapter/primer location, and adapter/primer length, NanoPrePro exerted a self-optimizing function to extract the best parameters in each sequencing file for users to customize their analyses. Furthermore, NanoPrePro shows a 38-times faster speed with less memory cost. NanoPrePro can be regarded as the state-of-the-art preprocessor with forward adaptability of ONT sequencing.

Indexed as

Gene Expression ProfilingHigh-Throughput Nucleotide SequencingNanopore SequencingSoftwareTranscriptomeAlgorithmsNanoporesSequence Analysis, RNAOxford nanopore technologiespreprocessingtranscriptome sequencing

Identifiers

PMID41686650
PMCPMC12903951

What Socratic holds

Textmetadata
LicenceCC BY
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.