Registration Open for Bioc2024 July 24-26


Working with Illumina Basecalling and Demultiplexing input and output files

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

Vignette Title HTML R Script
Reference Manual PDF


biocViews DataImport, Infrastructure, QualityControl, Sequencing, Software
Version 1.28.0
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)
See More
Suggests testthat, BiocStyle
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package basecallQC_1.28.0.tar.gz
Windows Binary
macOS Binary (x86_64) basecallQC_1.28.0.tgz
macOS Binary (arm64) basecallQC_1.28.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats