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

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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.
Funding Information
  • Ministry of Science and Technology of Taiwan (109-2636-B-002-003)
  • Ministry of Science and Technology of Taiwan (110-2628-B-002-026)
  • Ministry of Science and Technology of Taiwan (111-2628-B-002-020)
  • Ministry of Science and Technology of Taiwan (109-2636-B-010-008)
  • Ministry of Science and Technology of Taiwan (110-2636-B-A49A-502)
  • Ministry of Science and Technology of Taiwan (109-2636-B-006-009)
  • Ministry of Science and Technology of Taiwan (110-2636-B-006-008)
  • Ministry of Science and Technology of Taiwan (111-2636-B-006-015)
  • Taiwan National Science and Technology Council (112-2311-B-002-023-MY3)
  • Taiwan National Science and Technology Council (113-2628-B-002-023)
  • Taiwan National Science and Technology Council (114-2628-B-002-008)
  • Taiwan National Science and Technology Council (111-2628-B-A49-010)
  • Taiwan National Science and Technology Council (112-2320-B-A49-023)
  • Taiwan National Science and Technology Council (112-2636-B-006-006)
  • Taiwan National Science and Technology Council (113-2636-B-006-004)
  • Yen Tjing Ling Medical Foundation (CI-113-3)
  • Yen Tjing Ling Medical Foundation (CI-114-14)

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