MiSeq Sequencer¶
This page contains information about handling MiSeq sequencer data.
MiSeq Run Structure¶
MiSeq runs typically have the following directory structure:
220101_M00001_0001_000000000-A1B2C/
├── Data/
├── InterOp/
├── Logs/
├── Recipe/
├── RTAComplete.txt
├── RunInfo.xml
├── RunParameters.xml
└── SampleSheet.csv
Required Files¶
The following files are required for processing MiSeq runs:
RunInfo.xml: Contains information about the run, including the run ID, instrument, flowcell, and read configuration.RunParameters.xml: Contains parameters used for the run, including chemistry, application version, and experiment name.SampleSheet.csv: Contains information about the samples in the run, including sample IDs, indices, and projects.RTAComplete.txt: Indicates that the run has completed.
Metadata Extraction¶
The following metadata is extracted from MiSeq runs:
- Run ID
- Instrument ID
- Flowcell ID
- Date
- Chemistry
- Application version
- Sample count
- Read configuration
Workflow¶
The MiSeq ingest workflow performs the following steps:
- Find completed MiSeq runs
- Validate the run structure
- Extract metadata from the run files
- Upload the run to iRODS
- Add metadata to the iRODS collection
For more information, see the Workflows section.