DOI: 10.18129/B9.bioc.FastqCleaner    

This is the development version of FastqCleaner; for the stable release version, see FastqCleaner.

A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

Bioconductor version: Development (3.15)

An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.

Author: Leandro Roser <learoser at>, Fernán Agüero <learoser at>, Daniel Sánchez <learoser at>

Maintainer: Leandro Roser <learoser at>

Citation (from within R, enter citation("FastqCleaner")):


To install this package, start R (version "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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biocViews QualityControl, SangerSeq, SequenceMatching, Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 3.8 (R-3.5) (3 years)
License MIT + file LICENSE
Imports methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
LinkingTo Rcpp
Suggests BiocStyle, testthat, knitr, rmarkdown
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