NanoPrePro Documentation

NanoPrePro is a pre-processor for Oxford Nanopore transcriptomic sequencing data.

Contents:

• Installation
  • Option 1: run with Docker
  • Option 2: use pip install
• Implementation
  • Quick start
  • Pre-processing pipeline
• Output
  • Processed FASTQ
  • HTML report

Citation

If you use NanoPrePro in your research, please cite:

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, Ying-Lan Chen, Hsin-Hung Lin, Jung-Chen Su, Ying-Chung Jimmy Lin, NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing, Briefings in Bioinformatics, Volume 27, Issue 1, January 2026, bbag063, https://doi.org/10.1093/bib/bbag063