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FastqCleaner

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


Bioconductor version: Release (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FastqCleaner")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FastqCleaner")
An Introduction to FastqCleaner HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews QualityControl, SangerSeq, SequenceMatching, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License MIT + file LICENSE
Depends
Imports methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
System Requirements
URL
See More
Suggests BiocStyle, testthat, knitr, rmarkdown
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package FastqCleaner_1.20.0.tar.gz
Windows Binary FastqCleaner_1.20.0.zip
macOS Binary (x86_64) FastqCleaner_1.20.0.tgz
macOS Binary (arm64) FastqCleaner_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FastqCleaner
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FastqCleaner
Bioc Package Browser https://code.bioconductor.org/browse/FastqCleaner/
Package Short Url https://bioconductor.org/packages/FastqCleaner/
Package Downloads Report Download Stats