Aozan works in 6 steps. It sends mails at each step of the pre-analysis workflow and a QC report at the end of the quality control step. The parameters for each step should be written in Aozan configuration file, an example is here. The available steps are:
- New run discovering
- sends an email, if a new run is currently running. For sequencers that use RTA 1.x, sends in attachment the first base report
- End of run detection
- Checks "
Basecalling_Netcopy_complete.txt" file creation in the run directory - Can handle multiple sequencer outputs
- Checks "
- NAS and mid-term storage synchronization (Optional step)
- Uses rsync
- Does not copy CIF files (optional)
- Demultiplexing
- Demultiplexing is performed by Bcl2fastq 2.x
- Parallel computation
- Creates one fastq file by sample
- Uses alias for samples indexes (optional)
- Quality control and validation
- Global quality tests on general sequencing data
- Lane quality tests on demultiplexing step data
- Project quality tests on demultiplexing step data
- Sample quality tests on demultiplexing step data
- Pooled sample quality tests on demultiplexing step data
- Creates a QC report file with thresholds for acceptable values