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Background  Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.    Results  This paper presents  FastqCleaner,  a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework.  FastqCleaner  combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.    Conclusions   FastqCleaner  is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes  FastqCleaner  a valuable resource for NGS data analysis.    Electronic supplementary material  The online version of this article (10.1186/s12859-019-2961-8) contains supplementary material, which is available to authorized users.

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files