Illumina HiSeq/GAIIx Instrument Interface
To ensure that your Illumina instrument warranty remains valid, this integration must be performed and maintained by the Platform SW BaseSpace Clarity LIMS support team as needed.
Overview of the Platform SW BaseSpace Clarity LIMS ↔ Illumina HiSeq/GAIIx Instrument Interface
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Image Action #
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Description
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0
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Illumina Sequencing (Illumina SBS) 4.0 initiated in Platform SW BaseSpace Clarity LIMS.
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1
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1.
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Begin Run event fires on Illumina instrument. |
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2.
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Instrument fires configured LIMS script. |
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3.
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Script writes Begin Run event to Network Attached Storage (NAS) root folder in \gls_events . |
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2
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1.
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Timer-based daemon on Clarity LIMS server wakes up and looks for events. |
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2.
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Daemon discovers Begin Run event and processes it. |
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3.
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Daemon uses the supplied process run directory to locate the run folder on the NAS. |
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4.
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Daemon parses key information from the run folder, including the Flowcell ID. |
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5.
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Daemon uses Clarity LIMS REST API to do the following: |
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Locate the sequencing process for this flow cell (based on ID). |
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•
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Run Type, Control Lane, Flowcell ID, Flowcell Position, Flowcell Version, Experiment Name, Read 1 Cycles, Index 1 Read Cycles, Index 2 Read Cycles, Read 2 Cycles, Output Folder, Run ID, TruSeq SBS Kit lot #, TruSeq SBS Kit Type |
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–
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Examine list of files to collect, and attach any that are now available: |
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•
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RunInfo.xml, runParameters.xml (or RTAConfiguration.xml), Link to Run Folder.html |
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3
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1.
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Cycle Complete event fires on Illumina instrument. |
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2.
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Instrument fires configured Clarity LIMS script. |
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3.
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Script writes Cycle Complete event to NAS network root folder in \gls_events . |
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4
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1.
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Timer-based daemon on Clarity LIMS server wakes up and looks for events. |
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2.
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Daemon discovers Cycle Complete event and processes it. |
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3.
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Daemon uses the supplied process run directory to locate the run folder on the NAS. |
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4.
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Daemon parses key information from the run folder, including the Flowcell ID. |
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5.
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Daemon uses Clarity LIMS REST API to do the following: |
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•
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Status – populate with cycle information (e.g., Cycle 18 of 36) |
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–
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Examine list of files to collect, and attach any that are now available: |
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•
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Re-checks for any other files that may not have been available at Begin Run event. |
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–
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On Cycle 25 of standard output runs, Clusters PF R1 and %PF R1 run statistics are calculated from the binary InterOp files and stored in Output UDFs on the sample analytes in the flow cell (generated by Cluster Generation). |
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5
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1.
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End Run event fires on Illumina instrument. |
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2.
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Instrument fires configured Clarity LIMS script. |
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3.
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Script writes End Run event to NAS network root folder in \gls_events . |
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6
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1.
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Timer-based daemon on Clarity LIMS server wakes up and looks for events. |
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2.
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Daemon discovers End Run event and processes it. |
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3.
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Daemon uses the supplied process run directory to locate the run folder on the NAS. |
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4.
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Daemon parses key information from the run folder including the Flowcell ID . |
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5.
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Daemon uses Clarity LIMS REST API to do the following: |
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–
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Examine list of files to collect, and attach any that are now available: |
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•
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Final check for any files available that are not already attached. |
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–
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Run statistics are parsed from several binary InterOp files and are stored (visible in the Illumina Sequencing run). |
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–
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Run Report invoked, generated, and attached. T his report highlights metrics with values that are >1 std. deviation outside the average calculated from the past 5 runs on that specific instrument. |
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7
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After sequencing, a lab scientist runs a Bcl conversion process invoking EPP to:
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1.
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Retrieve necessary system data via the REST API and the network run directory from the sequencing process. |
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2.
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Invoke Bcl conversion using previously stored network run directory, SampleSheet.csv (generated by theCluster Generation process) file, and any parameters specified in process UDFs. |
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3.
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Demultiplexing of data takes place directly within the network run directory by the Illumina Bcl software—as would be the case if Clarity LIMS did not initiate it. |
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8
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At the conclusion of the EPP dispatched job (and the Bcl conversion it initiates) some lightweight but important data is captured:
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•
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HTML Link files to the FASTQ reads (the actual FASTQ reads are now in the run directory on the NAS) |
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