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BMC Bioinformatics. 2019 Jun 28;20(1):361. doi: 10.1186/s12859-019-2961-8.

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

Author information

1
Instituto de Investigaciones Biotecnológicas (IIB), Universidad Nacional de San Martín - CONICET, 25 de Mayo 1401, B1650HMP, San Martín, Buenos Aires, Argentina. learoser@gmail.com.
2
Instituto de Investigaciones Biotecnológicas (IIB), Universidad Nacional de San Martín - CONICET, 25 de Mayo 1401, B1650HMP, San Martín, Buenos Aires, Argentina.
3
Instituto de Investigaciones Biotecnológicas (IIB), Universidad Nacional de San Martín - CONICET, 25 de Mayo 1401, B1650HMP, San Martín, Buenos Aires, Argentina. dsanchez21@gmail.com.

Abstract

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.

KEYWORDS:

Bioconductor; FASTQ; Next generation sequencing; R; Shiny; User-friendly tool; Visualization; Web app

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