basecallQC

DOI: 10.18129/B9.bioc.basecallQC    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see basecallQC.

Working with Illumina Basecalling and Demultiplexing input and output files

Bioconductor version: 3.9

The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Author: Thomas Carroll and Marian Dore

Maintainer: Thomas Carroll <tc.infomatics at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("basecallQC")

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("basecallQC")

 

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Infrastructure, QualityControl, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL (>= 3)
Depends	R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml
Imports	ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead
LinkingTo
Suggests	testthat, BiocStyle
SystemRequirements	bcl2Fastq (versions >= 2.1.7)
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	basecallQC_1.8.0.tar.gz
Windows Binary	basecallQC_1.8.0.zip
Mac OS X 10.11 (El Capitan)	basecallQC_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/basecallQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/basecallQC
Package Short Url	https://bioconductor.org/packages/basecallQC/
Package Downloads Report	Download Stats