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
    • 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

Global quality control tests

User can add global 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. Usually the global tests reuse data collected from lane tests or sample tests. Please report to those documentation pages for more information. You will find below all the parameters for all the available tests in Aozan:

Configuration global quality tests

Aozan property	Type	Default value	Description
qc.test.global.base.count.enable	boolean	False	Enable global base count test
qc.test.global.base.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.non.indexed.base.count.enable	boolean	False	Enable global non indexed global base count test
qc.test.global.non.indexed.base.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.raw.cluster.count.enable	boolean	False	Enable global raw cluster count test
qc.test.global.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.mean.raw.cluster.count.enable	boolean	False	Enable global mean raw cluster count test
qc.test.global.mean.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.median.raw.cluster.count.enable	boolean	False	Enable global median raw cluster count test
qc.test.global.median.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.raw.cluster.sd.enable	boolean	False	Enable global raw cluster standard deviation test
qc.test.global.raw.cluster.sd.interval	integer interval	Not set	Interval for valid values
qc.test.global.pf.cluster.count.enable	boolean	False	Enable global passing filter cluster count test
qc.test.global.pf.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.mean.pf.cluster.count.enable	boolean	False	Enable global mean passing filter cluster count test
qc.test.global.mean.pf.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.median.pf.cluster.count.enable	boolean	False	Enable global median passing filter cluster count test
qc.test.global.median.pf.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.pf.cluster.sd.enable	boolean	False	Enable global passing filter cluster standard deviation test
qc.test.global.pf.cluster.sd.interval	integer interval	Not set	Interval for valid values
qc.test.global.pf.cluster.percent.enable	boolean	False	Enable global passing filter percent test
qc.test.global.pf.cluster.percent.interval	double interval	Not set	Interval for valid values
qc.test.global.phix.align.percent.enable	boolean	False	Enable global PhiX align percent test
qc.test.global.phix.align.percent.interval	integer interval	Not set	Interval for valid values
qc.test.global.phix.raw.cluster.count.enable	boolean	False	Enable global PhiX raw cluster count test
qc.test.global.phix.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.mean.phix.raw.cluster.count.enable	boolean	False	Enable global mean PhiX raw cluster count test
qc.test.global.mean.phix.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.median.phix.raw.cluster.count.enable	boolean	False	Enable global median PhiX raw cluster count test
qc.test.global.median.phix.raw.cluster.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.phix.raw.cluster.sd.enable	boolean	False	Enable global PhiX raw cluster standard deviation test
qc.test.global.phix.raw.cluster.sd.interval	integer interval	Not set	Interval for valid values
qc.test.global.undetermined.cluster.percent.enable	boolean	False	Enable global undetermined cluster percent test
qc.test.global.undetermined.cluster.percent.interval	integer interval	Not set	Interval for valid values
qc.test.global.cycle.count.enable	boolean	False	Enable global cycle count test
qc.test.global.cycle.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.lane.count.enable	boolean	False	Enable global lane count test
qc.test.global.lane.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.project.count.enable	boolean	False	Enable global project count test
qc.test.global.project.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.sample.count.enable	boolean	False	Enable global sample count test
qc.test.global.sample.count.interval	integer interval	Not set	Interval for valid values
qc.test.global.error.rate.enable	boolean	False	Enable global error rate test
qc.test.global.error.rate.interval	double interval	Not set	Interval for valid values
qc.test.global.cluster.density.enable	boolean	False	Enable global cluster density test
qc.test.global.cluster.density.interval	double interval	Not set	Interval for valid values
qc.test.global.cluster.density.pf.enable	boolean	False	Enable global cluster passing filter density test
qc.test.global.cluster.density.pf.interval	double interval	Not set	Interval for valid values
qc.test.global.q30.percent.enable	boolean	False	Enable global Q30 percent test
qc.test.global.q30.percent.interval	double interval	Not set	Interval for valid values
qc.test.global.occupancy.percent.enable	boolean	False	Enable global occupancy percent test
qc.test.global.occupancy.percent.interval	double interval	Not set	Interval for valid values
qc.test.global.loading.concentration.percent.enable	boolean	False	Enable global loading concentration percent test
qc.test.global.loading.concentration.percent.interval	double interval	Not set	Interval for valid values

An example of table built with lanes global 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