FastqCleaner

DOI: 10.18129/B9.bioc.FastqCleaner    

This is the development version of FastqCleaner; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("FastqCleaner", version = "devel")

Documentation

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

browseVignettes("FastqCleaner")

 

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

Details

biocViews QualityControl, SangerSeq, SequenceMatching, Sequencing, Software
Version 0.99.39
License GPL (>= 2)
Depends
Imports methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, methods, 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
Build Report  

Package Archives

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

Source Package FastqCleaner_0.99.39.tar.gz
Windows Binary FastqCleaner_0.99.39.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) FastqCleaner_0.99.39.tgz
Source Repository git clone https://git.bioconductor.org/packages/FastqCleaner
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FastqCleaner
Package Short Url http://bioconductor.org/packages/FastqCleaner/
Package Downloads Report Download Stats

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