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

## TL;DR

NanoPrePro is a fast and efficient tool for processing nanopore sequencing data, offering better performance than existing methods.

## Contribution

NanoPrePro introduces a self-optimizing function and is significantly faster and more memory-efficient than current tools.

## Key findings

- NanoPrePro outperforms Pychopper in simulated and real datasets.
- It is 38 times faster with lower memory usage.
- The tool offers customizable parameters for better precision in read preprocessing.

## 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.