FastqCleaner

DOI: 10.18129/B9.bioc.FastqCleaner  

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

Bioconductor version: Release (3.16)

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>

Installation

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

 

HTML	R Script	An Introduction to FastqCleaner
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	QualityControl, SangerSeq, SequenceMatching, Sequencing, ShinyApps, Software
Version	1.16.1
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	MIT + file LICENSE
Depends
Imports	methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
LinkingTo	Rcpp
Suggests	BiocStyle, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	FastqCleaner_1.16.1.tar.gz
Windows Binary	FastqCleaner_1.16.1.zip
macOS Binary (x86_64)	FastqCleaner_1.16.1.tgz
macOS Binary (arm64)	FastqCleaner_1.16.1.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
Old Source Packages for BioC 3.16	Source Archive