Sample Sheet Generation

Package Version: BaseSpace Clarity LIMS MiSeqDx (v1.10.0)

Overview

The Illumina MiSeqDx Integration Package allows for automatic generation of a sample sheet to be used with the MiSeqDx instrument software. The format of this sample sheet is designed for the instrument when it is running in Diagnostic mode.

Note

• If you are running the MiSeqDx instrument in Research Use Only (RUO) mode, see Sample Sheet Generation section in the Configuration guide for MiSeq version-of-interest.

• MiSeqDx does not support bcl2fastqv2 sample sheet generation.

How sample sheet generation works

Sample sheet generation is configured on the step prior to the sequencing run – Denature, Dilute and Load Sample, which is the step where samples are placed on the flow cells or reagent cartridges that will be placed in the instrument.

The sample sheet is generated by means of a script, which the lab user initiates by clicking a button on the Record Details screen of the step. This generates a sample sheet file for the container loaded during the step, where the name of the sample sheet will be

<reagent cartridge barcode ID>.csv

The user then downloads the sample sheet from the LIMS and uploads it to the instrument software.

MiSeqDx Assays Support

The following assays are supported by the MiSeqDx sample sheet generation script:

• CF 139-Variant Assay

• CF Clinical Sequencing Assay

• Universal Kit

Configured Master Step Fields/Step UDFs

Sample sheet format is controlled via master step field / step user defined field (UDF) configuration, where key step fields are pre-populated with values specific to each protocol step. These values are not editable, and their configuration should not be modified.

For details, see Sample Sheet Data and File Format and Contents sections below.

The fields listed in the following table are available on the Denature, Dilute and Load Sample step and will be placed into the sample sheet.

Submitted Sample Global Fields/UDFs

Script Parameters and Usage

Usage

Below is the default command line that ships with the Denature, Dilute and Load Sample (CF 139-Variant Assay) step.

bash -c "/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' && /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 && /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'"

Support for Container Types

Single well container types, and all one-dimensional container types with both numeric rows and numeric columns, are supported.

Sample Sheet Data

The following table lists and describes the fields included in the MiSeqDx sample sheet.

Note the following:

• If no upstream pooling is detected, LIMS will populate the sample sheet with the SampleID and SampleName of the submitted sample. Other fields are populated with data from the samples that were input to the step (i.e. derived samples).

• If upstream pooling is detected, LIMS will populate the sample sheet with the first upstream pooled inputs found – not with the submitted sample or step input fields.

Control samples may be one of the following:

• Built-in BaseSpace Clarity LIMS control samples

• Submitted samples with field / UDF Control? set to true

Header Section

Manifests Section

Reads Section

Settings Section

Data Section

File Format and Contents

This section outlines the format and contents of the generated sample sheet and associated log file.

When validating the installation of your integration, refer to this information to ensure that the sample sheet and log files are correctly generated.

MiSeqDx sample sheet

• The file is a comma-separated file.

• The file contains the following sections:

  • Header

  • Manifests

  • Reads

  • Settings

  • Data

• The file is populated with data from the samples in the step. If pooled, each sample in the pool is represented as a separate, demultiplexed entry.

• The entries are sorted by SampleWell and by SampleID.

• The data section of the file contains 11 columns.

MiSeqDx sample sheet log file

• The file is in HTML format.

• The file contains logging information and a success message if sample sheet generated successfully.

Configuration Options

Enabling unique FASTQ file names

To enable unique FASTQ file names per sequencing run, the EPP command on the process type must be configured to use the following parameter options:

• -useSampleLimsID – ensures unique entries in the SampleName column by using the sample LIMS ID instead of its name

• -appendLimsID – ensures unique names per run by appending the LIMS ID of the current step

For more information, see Script Parameters and Usage.

Rules and Constraints

• The step on which this script runs must be the step in which samples are placed on the flow cell(s) or reagent cartridge(s).

• The contents of the sample sheet are ordered by SampleWell and then ordered by SampleID.

• Project and sample names in the sample sheet cannot contain illegal characters. Characters not allowed are the space character and the following: ? ( ) [ ] / \ = + < > : ; " ' , * ^ | &

• Illegal characters will be replaced with an underscore "_"

• The destination container type (flow cell or reagent cartridge) must be must be either single well or a one-dimensional container type with both numeric rows and numeric columns. Back to top