DOI: 10.18129/B9.bioc.FastqCleaner  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see FastqCleaner.

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

Bioconductor version: 3.17

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 [aut, cre], Fernán Agüero [aut], Daniel Sánchez [aut]

Maintainer: Leandro Roser <learoser at>

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


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HTML R Script An Introduction to FastqCleaner
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biocViews QualityControl, SangerSeq, SequenceMatching, Sequencing, Software
Version 1.18.0
In Bioconductor since BioC 3.8 (R-3.5) (5 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
Depends On Me
Imports Me
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