Sample Sheet Generation

In each Illumina SBS MiSeqDx and Validation protocol, automated sample sheet generation is configured on the Record Details screen of the Denature, Dilute and Load Sample 1.1 step. This is when the samples are loaded onto the container that will be placed in the instrument.

The integration allows for generation of a sample sheet designed to be used with the MOS (Diagnostic mode) instrument software.

By default, one MiSeqDx instrument sample sheet is created for the reagent cartridge loaded during the step. The placeholders and sample sheet files in the following table are generated by the Denature, Dilute and Load Sample 1.1 step.

Item

Description

Lab Tracking Form placeholder

This placeholder allows you to manually attach a lab-specific tracking form to the step.

MiSeqDx Sample Sheet file
• This CSV file is automatically generated by the LIMS for use with the MOS or MCS software.
• May be opened as a text file, or as an MS Excel spreadsheet.

MiSeqDx Sample Sheet Generation Log

Automatically generated by Clarity LIMS, this log file captures any errors encountered when generating the MiSeqDx sample sheet (MOS).

The sample sheet generation automation is configured on the Record Details screen of the Denature, Dilute and Load Sample 1.1 step.

• This automation is triggered by a button on the Record Details screen.
• The automation sets the value of the Progress field on the sample to 'Library ready for sequencing'.

/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {processURI:v2} script:setUDF -f 'Progress' -t '//input/@uri->//sample/@uri' -v 'Library ready for sequencing'

• The automation starts a script that generates the sample sheet.

&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/miseqdx/miseqdx-extensions.jar -u {username} -p {password} -i {processURI:v2} script:generate_miseqdx_sample_sheet -c {compoundOutputFileLuid1} -e {compoundOutputFileLuid2} --useSampleLimsID true --isMiSeqDx true

To maintain unique values in the Sample_Name column of the sample sheet, the sample sheet generation automation script has the useSampleLimsID parameter set to true. The appendLimsID parameter must not be set to true.

For the automation to display the correct instrument name when it is completed, the --isMiSeqDx parameter must be set to true.

• The automation labels the derived samples that do not have reagent labels. The label value applied is NoIndex.

&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {processURI:v2} script: labelNonLabeledOutputs -l 'NoIndex'

See MiSeqDx Integration v1.9 Validation and Troubleshooting.

For more information on sample sheet generation, including details on file format and contents, master step and global fields, script parameters, and configuration options, see the following documentation:

• Illumina MiSeqDx 1.x Sample Sheet Generation—For details on the Diagnostic mode sample sheet designed for use with MOS software.
• Sample Sheet Generation—For details on the Research mode sample sheet designed for use with MCS software.