About Aozan

• What is Aozan ?
• Licenses
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• 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
    • Global tests
    • Lane tests
    • Project tests
    • Sample tests
    • Pooled sample tests
• Known bugs
• Mailing list

Development

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

Lanes quality control tests

User can add lane tests to be performed in this steps. The order of the parameters in the Aozan configuration file will be reused in the report generated by this step. Each test can use several parameters and contains always an "enable" property to activate the test. Usually a property named "interval" exists for each test, however if this property is not set, the value will be computed but not checked if it is the correct interval. You will find below all the parameters for all the available tests in Aozan:

Parameters for collect data to lanes quality tests

Aozan property	Type	Default value	Description
qc.conf.cluster.density.ratio	integer	0.3472222	Value necessary for compute the cluster density in the lane quality tests

Configuration lanes quality tests

Aozan property	Type	Default value	Description
qc.test.lane.raw.cluster.count.enable	boolean	False	Enable lane raw cluster count test
qc.test.lane.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.lane.pf.cluster.count.enable	boolean	False	Enable lane passing filter cluster count test
qc.test.lane.pf.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.lane.pf.cluster.percent.enable	boolean	False	Enable lane passing filter cluster percent test
qc.test.lane.pf.cluster.percent.interval	double interval	Not set	Interval for valid values
qc.test.lane.yield.enable	boolean	False	Enable lane yield test
qc.test.lane.yield.interval	integer interval	Not set	Interval for valid values
qc.test.lane.yield.pf.enable	boolean	False	Enable lane yield passing filter test
qc.test.lane.yield.pf.interval	integer interval	Not set	Interval for valid values
qc.test.lane.phix.raw.cluster.count.enable	boolean	False	Enable lane PhiX raw cluster count test
qc.test.lane.phix.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.lane.cluster.density.enable	boolean	False	Enable lane cluster density test
qc.test.lane.cluster.density.interval	double interval	Not set	Interval for valid values
qc.test.lane.cluster.density.pf.enable	boolean	False	Enable lane cluster passing filter density test
qc.test.lane.cluster.density.pf.interval	double interval	Not set	Interval for valid values
qc.test.lane.phix.align.percent.enable	boolean	False	Enable lane PhiX align percent test
qc.test.lane.phix.align.percent.interval	double interval	Not set	Interval for valid values
qc.test.lane.error.rate.enable	boolean	False	Enable lane error rate test
qc.test.lane.error.rate.interval	double interval	Not set	Interval for valid values of lane error rate
qc.test.lane.35.cycle.error.rate.enable	boolean	False	Enable lane 35 cycle error rate test
qc.test.lane.35.cycle.error.rate.interval	double interval	Not set	Interval for valid values
qc.test.lane.75.cycle.error.rate.enable	boolean	False	Enable lane 75 cycle error rate test
qc.test.lane.75.cycle.error.rate.interval	double interval	Not set	Interval for valid values
qc.test.lane.100.cycle.error.rate.enable	boolean	False	Enable lane 100 cycle error test
qc.test.lane.100.cycle.error.rate.interval	double interval	Not set	Interval for valid values
qc.test.lane.first.cycle.intensity.enable	boolean	False	Enable lane first cycle intensity test
qc.test.lane.first.cycle.intensity.interval	integer interval	Not set	Interval for valid values
qc.test.lane.cycle.20.intensity.percent.enable	boolean	False	Enable lane cycle 20 intensity percent test
qc.test.lane.cycle.20.intensity.percent.interval	double interval	Not set	Interval for valid values
qc.test.lane.phasing.prephasing.percent.enable	boolean	False	Enable lane phasing prephasing percent test
qc.test.lane.phasing.prephasing.percent.phasing.interval	double interval	Not set	Interval for valid values of lane phasing percent
qc.test.lane.phasing.prephasing.percent.prephasing.interval	double interval	Not set	Interval for valid values of lane prephasing percent
qc.test.lane.q30.percent.enable	boolean	False	Enable lane Q30 percent test
qc.test.lane.q30.percent.interval	double interval	Not set	Interval for valid values
qc.test.lane.occupancy.percent.enable	boolean	False	Enable lane occupancy percent test
qc.test.lane.occupancy.percent.interval	double interval	Not set	Interval for valid values

An example of table built with lanes quality tests.

Syntax of the interval values

User can define intervals as the next examples:

• [,10] From - infinite to 10 (included)
• [,10[ From - infinite to 10 (excluded)
• [,10) From - infinite to 10 (excluded)
• ]2,10[ From 2 (excluded) to 10 (excluded)
• (2,10[ From 2 (excluded) to 10 (excluded)
• [2,10] From 2 (included) to 10 (included)
• [2, ] From 2 (included) to + infinite