FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of
Roser, L. G., Aguero, F. and Sanchez, D. O.
Instituto de Investigaciones Biotecnologicas (IIB), Universidad Nacional de San Martin - CONICET, 25 de Mayo 1401, B1650HMP, San Martin, Buenos Aires, Argentina. learoser@gmail.com.
Instituto de Investigaciones Biotecnologicas (IIB), Universidad Nacional de San Martin - CONICET, 25 de Mayo 1401, B1650HMP, San Martin, Buenos Aires, Argentina.
Instituto de Investigaciones Biotecnologicas (IIB), Universidad Nacional de San Martin - CONICET, 25 de Mayo 1401, B1650HMP, San Martin, Buenos Aires, Argentina. dsanchez21@gmail.com.
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.
BMC Bioinformatics 20(1): 361 (2019)