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basecallQC

This is the development version of basecallQC; for the stable release version, see basecallQC.

Working with Illumina Basecalling and Demultiplexing input and output files


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Vignette Title HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, Infrastructure, QualityControl, Sequencing, Software
Version 1.27.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
System Requirements bcl2Fastq (versions >= 2.1.7)
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Package Archives

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

Source Package basecallQC_1.27.0.tar.gz
Windows Binary basecallQC_1.27.0.zip
macOS Binary (x86_64) basecallQC_1.27.0.tgz
macOS Binary (arm64) basecallQC_1.27.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/basecallQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/basecallQC
Bioc Package Browser https://code.bioconductor.org/browse/basecallQC/
Package Short Url https://bioconductor.org/packages/basecallQC/
Package Downloads Report Download Stats