Quality control step
This step allows to perform quality controls on the output runs. To do this Aozan uses Illumina reports, FastQC results and contamination detection results (using a reimplementation of FastQ Screen).
This step creates a report file including the thresholds fixed for quality controls with :
- Global quality tests with Illumina reports
- Lane quality tests with Illumina reports
- Project quality tests with Illumina reports, demultiplexing reports and optional samples reports. Data is aggregated by project
- Samples quality tests with Illumina reports, FastQC, contamination detection and clusting recovering estimation with more demultiplexing mismatches
- Pooled sample quality tests with Illumina reports, demultiplexing reports and optional samples reports. Data is aggregated by technical replicates
Note: The quality control step is the longest step, it can last several hours/days. If Aozan is stopped before the end of this step, it is possible to relaunch it. Restore points allow get back at the last sample processed.
Configuration parameters
The next table contains the parameters of this step.
| Aozan property | Type | Default value | description |
|---|---|---|---|
| qc.step | boolean | True | Enable the step. If True, at least one test must be enabled, otherwise no data will be collected for the QC report. |
| qc.step.end.email.template | string | Not set | Path of the email template for the end of the qc step. |
| qc.report.save.raw.data | boolean | False | Save raw data generated for the tests |
| qc.report.save.report.data | boolean | False | Save report data in XML format (before applying the stylesheet) |
| qc.report.stylesheet | string | Not set | Path to the XSL stylesheet to use |
| qc.report.tests.to.remove.in.basic.report | string | Not set | A list of test (e.g. qc.test.lane.pf.cluster.count) separated by commas to remove from an additional HTML report.
This second HTML report will have the same filename as the standard HTML report but with "-basic" suffix before the HTML extension. |
| qc.conf.threads | integer | The number of core available on the system | The number of thread to use |
An example of email sent to the end of Aozan with the quality control summary as attachment and an example of all data built for one run in quality control step.
Aozan creates a html page to navigate in all documents and archives from a run.
