PT  - JOURNAL ARTICLE
AU  - Leandro Gabriel Roser
AU  - Fernán Agüero
AU  - Daniel Oscar Sánchez
TI  - FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
AID  - 10.1101/393140
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 393140
4099  - http://biorxiv.org/content/early/2018/08/16/393140.short
4100  - http://biorxiv.org/content/early/2018/08/16/393140.full
AB  - 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.NGSNext Generation SequencingSRSingle-ReadsPEPaired-End Reads