FastqCleaner

DOI: 10.18129/B9.bioc.FastqCleaner    

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

Bioconductor version: Release (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 = "3.8")

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 1.0.0
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
Links To Me
Build Report  

Package Archives

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

Source Package FastqCleaner_1.0.0.tar.gz
Windows Binary FastqCleaner_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) FastqCleaner_1.0.0.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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