NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing
Journal
Briefings in Bioinformatics
Journal Volume
27
Journal Issue
1
Start Page
bbag063
ISSN
1467-5463
1477-4054
Date Issued
2026-02-13
Author(s)
Chu, Chia-Chen
Yu, Jhong-He
Kuo, Shang-Che
Yang, Fan-Wei
Lin, Chia-Chang
Chen, Chang-Hung
Wu, Yi-Chen
Shih, Cing
Sun, Ying-Hsuan
Chen, Ying-Lan
Lin, Hsin-Hung
Su, Jung-Chen
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.
Subjects
Oxford nanopore technologies
preprocessing
transcriptome sequencing
Publisher
Oxford University Press (OUP)
Type
journal article