About Aozan

• What is Aozan ?
• Licenses
• People behind Aozan
• How to cite Aozan

Getting Aozan

• Downloading
• Installing
• Release Notes
• Samplesheet validator
• Quality report example

Documentation

• Quickstart Guide
• Example data
• Built-in steps
  • First base report
  • End run discovering
  • Synchronization
  • Demultiplexing
  • Quality Control
• Known bugs
• Mailing list

Development

• How to contribute
• Writing a plugin
• Downloading sources
• Compiling
• Aozan on GitHub
• Javadoc

The demultiplexing step

This step allows to launch demultiplexing using bcl2fastq 2.x. Aozan can use samplesheets in XLS or XLSX format or generated by an external tool in addition of samplesheets in CSV format. Using a samplesheet in XLS or XLSX format allows to use aliases for adapter sequence indexes. A template of bcl2fastq samplesheet file in XLS format can be found Here.

If not using an external tool to build the samplesheet, the samplesheet must be created in a dedicated directory using a standardized name (e.g. samplesheet_SNL177_0153.xls where SNL177 is the name of the sequencer provided by the run id, and 0153 is the run number.

If no samplesheet file is provided in the dedicated directory, Aozan will use if it exists, the SampleSheet.csv file at the root of the run directory. The SampleSheet.csv file is created by the sequencer control software when the user provides a samplesheet at the run startup.

Alongside Aozan, we provide a standalone Bcl2fastq samplesheet validator available on our website that allows you to check your run samplesheet and generate a valid CSV samplesheet file. The validator is available here.

Configuration parameters

The following table contains the parameters for this step.

Aozan property	Type	Default value	description
demux.step	boolean	True	Enable the step
demux.tool	string	bcl2fastq	Tool to use for demultiplexing (available values: bcl2fastq or bclconvert)
demux.use.hiseq.output	boolean	False	If this parameter is set to true and if the synchronization step is not enabled, this step will use directly the sequencer output for demultiplexage step
demux.space.factor	double	0.7	Factor to use to get the estimation of the amount of space needed in the fastq directory for the run based on the amount of space used in the bcl directory by the run data
index.sequences	string	Not set	Path to a file containing aliases for adapter sequence indexes. See an example
samplesheet.format	string	xls	Bcl2fastq samplesheet format ("csv", "xls", "xlsx", or "command")
samplesheet.prefix	string	samplesheet	Prefix for Bcl2fastq samplesheet file
samplesheet.generator.command	String	Not set	Command to execute to generate the Bcl2fastq samplesheet in CSV format when the parameter bcl2fastq.samplesheet.format is set to "command"
samplesheet.path	string	Not set	Path to CSV/XLS/XLSX samplesheet files.
bcl2fastq.mismatches	integer	0	Number of mismatches allowed in adapter indexes. This value is overrided by the MismatchCount setting in the samplesheet
bcl2fastq.adapter.fasta.file.path	string	Not set	Adapter sequence file to use when bcl2fastq is launched
bcl2fastq.path	string	/usr/local/bcl2fastq	Path to Bcl2fastq binary
bcl2fastq.with.failed.reads	boolean	True	Add the reads that do not pass Illumina filter in the FASTQ files
bcl2fastq.additionnal.arguments	string	Not set	Additional arguments for Bcl2fastq
bcl2fastq.threads	integer	Number of computer cores	Number of threads to use for demultiplexing
bclconvert.path	string	/usr/bin/bcl-convert	Path to BCL Convert binary

Configuring Bcl2fastq barcode mismatches in the samplesheet

With Aozan, you can define the number of barcode mismatches to use with Bcl2fastq by adding a entry named MismatchCount in your Settings section of the samplesheet. This value will override the bcl2fastq.mismatches value set in the Aozan configuration file.

Configuration required to run bcl2fastq or BCL Convert with Docker images.

This Aozan version can run Docker image for demultiplexing step. On our platform, we build a new image for each bcl2fastq new version. They can be downloaded from the genomic paris centre repository.

Aozan property	Type	Default value	Description
bcl2fastq.use.docker	boolean	True	Enable to use Docker container to run bcl2fastq for demultiplexing.
bcl2fastq.docker.image	string	Not set	Docker image to use for bcl2fastq.
bclconvert.use.docker	boolean	True	Enable to use Docker container to run BCL Convert for demultiplexing.
bclconvert.docker.image	string	Not set	Docker image to use for BCL Convert.
docker.uri	string	unix:///var/run/docker.sock	Docker deamon URI.

An example of email sent at the end of demultiplexing step.

• Example on HiSeq 1500