FastProNGS: Fast Preprocessing of Next-Generation Sequencing Reads

Chao Wu, Xiaoshuang Liu, Zhenhe Yan, Yang Yang, Xiaomin Li, Guangxin Zhang

Research output: Contribution to journalArticlepeer-review

12 Scopus Citations


Background: Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. Results: We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. Conclusions: FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is also very flexible and can implement different functions using different user-set parameter combinations.

Original languageAmerican English
Article number345
Number of pages6
JournalBMC Bioinformatics
Issue number1
StatePublished - 2019

Bibliographical note

Publisher Copyright:
© 2019 The Author(s).

NREL Publication Number

  • NREL/JA-2700-74302


  • Adapter removing
  • NGS
  • Quality control


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