Illumina MiSeq Instrument Interface

Note:

To ensure that your Illumina instrument warranty remains valid, this integration must be performed and maintained by the BaseSpace Clarity LIMS Support team as needed.

Overview of the BaseSpace Clarity LIMS ↔ Illumina MiSeq Instrument Interface

Image Action #

Description

0

MiSeq Run (MiSeq) 4.0 initiated in the LIMS.

1

1. End Run event fires on Illumina instrument.
2. Instrument fires configured LIMS script.
3. Script writes End Run event to Network Attached Storage (NAS) root folder in \gls_events .

2

1. Timer-based daemon on the LIMS server wakes up and looks for events.
2. Daemon discovers End Run event and processes it.
3. Daemon uses the supplied process run directory to locate the run folder on the NAS.
4. Daemon parses key information from the run folder, including the Reagent Cartridge ID.
5. Daemon uses the LIMS REST API to do the following:
• Populate process UDFs: Finish Date, Run Type, Status, Flowcell ID, Flowcell Version, Experiment Name, Read 1 Cycles, Index 1 Read Cycles, Index 2 Read Cycles, Read 2 Cycles, Output Folder, Run ID, Reagent Cartridge ID, Reagent Cartridge Part #, PR2 Bottle ID, Chemistry, Workflow
• Examine list of files to collect, and attach any that are available:
– RunInfo.xml, runParameters.xml, Link to Run Folder.html
• Run statistics are parsed from several binary InterOp files and stored (visible in the MiSeq run).
• Illumina Run Report invoked, generated, and attached.