# Working with Illumina Basecalling and Demultiplexing input and output files

## Documentation for package ‘basecallQC’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

baseCallMetrics | Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).
basecallQC | The basecallQC object and constructor.
basecallQC-basecallQC | The basecallQC object and constructor.
basecallQC-class | The basecallQC object and constructor.
BCL2FastQparams | The Parameters for BCL2FastQparams object.
BCL2FastQparams-BCL2FastQparams | The Parameters for BCL2FastQparams object.
BCL2FastQparams-class | The Parameters for BCL2FastQparams object.
createBasemasks | Function to create basemasks for basecalling from Illumina samplesheet (for bcl2Fastq versions >= 2.1.7).
createBCLcommand | Function to create command for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7.
demultiplexMetrics | Gather demultiplexing metrics from a Run (using Run's DemultiplexingStats.xml file).
demuxBarplot | Barplot of Illumina demultiplexing statistics.
demuxBarplot-method | Barplot of Illumina demultiplexing statistics.
demuxBarplot.basecallQC | Barplot of Illumina demultiplexing statistics.
demuxBoxplot | Boxplot of Illumina demultiplexing statistics.
demuxBoxplot-method | Boxplot of Illumina demultiplexing statistics.
demuxBoxplot.basecallQC | Boxplot of Illumina demultiplexing statistics.
indexlengths | Index lengths
indexlengths,BCL2FastQparams-method, | Index lengths
indexlengths-method | Index lengths
indexlengths.bcl2fastqparams | Index lengths
interOpsReport | Function to parse InterOps files and generate summary reports
makeFQTable | Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead
passFilterBar | Barplot of Illumina basecalling statistics for reads passing filter.
passFilterBar-method | Barplot of Illumina basecalling statistics for reads passing filter.
passFilterBar.basecallQC | Barplot of Illumina basecalling statistics for reads passing filter.
passFilterBoxplot | Boxplot of Illumina basecalling statistics for reads passing filter.
passFilterBoxplot-method | Boxplot of Illumina basecalling statistics for reads passing filter.
passFilterBoxplot.basecallQC | Boxplot of Illumina basecalling statistics for reads passing filter.
passFilterTilePlot | Tile plot of Illumina basecalling statistics for reads passing filter.
passFilterTilePlot-method | Tile plot of Illumina basecalling statistics for reads passing filter.
passFilterTilePlot.basecallQC | Tile plot of Illumina basecalling statistics for reads passing filter.
readlengths | Read lengths
readlengths,BCL2FastQparams-method, | Read lengths
readlengths-method | Read lengths
readlengths.bcl2fastqparams | Read lengths
reportBCL | Generate basecallQC report
reportBCL-method | Generate basecallQC report
reportBCL.basecallQC | Generate basecallQC report
summaryConvStatsTable | Creates an HTML table of per sample summary statistics from basecalling results
summaryConvStatsTable-method | Creates an HTML table of per sample summary statistics from basecalling results
summaryConvStatsTable.basecallQC | Creates an HTML table of per sample summary statistics from basecalling results
summaryDemuxTable | Generate an HTML table of per sample summary demultiplexing statistics
summaryDemuxTable-method | Generate an HTML table of per sample summary demultiplexing statistics
summaryDemuxTable.basecallQC | Generate an HTML table of per sample summary demultiplexing statistics
validateBCLSheet | Illumina sample sheet cleaning and updating for bcl2Fastq versions >= 2.1.7