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BCL Convert

Supported Tool

bclconvert can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.


This BclConvert module is based on the bcl2fastq multiqc module. It can parse multiple bclconvert run outputs as long as they are from the same sequencing run. When doing this, the undetermined reads will be ‘corrected’ and re-calculated (as an unknown read from some one bclcovnert run might not be truly unknown, but simply from another run).

Calculate estimated depth

You can specify a genome size in config

It’s often useful to talk about sequencing yield in terms of estimated depth of coverage. In order to make MultiQC show the estimated depth for each sample, specify the reference genome/target size in your MultiQC configuration:

  genome_size: 3049315783

The coverage depth will be estimated as the yield Q30 dvivided by the genome size.

MultiQC comes with effective genome size presets for Human and Mouse, so you can provide the genome build name instead, like this: genome_size: hg38_genome. The following values are supported: hg19_genome, hg38_genome, mm10_genome.

Add barplots containing undetermined barcodes

By default, the bar plot of undetermined barcodes is only shown when reporting from a single demultiplexing run.

If you would like to show it with multiple runs (eg. bclconvert runs are split by lane), you can specify following parameter in your MultiQC config:

  create_undetermined_barcode_barplots: True

The default of this configuration value is False

File search patterns

  fn: RunInfo.xml
  fn: Demultiplex_Stats.csv
  fn: Quality_Metrics.csv
  fn: Adapter_Metrics.csv
  fn: Top_Unknown_Barcodes.csv