Configuration

The Illumina NextSeq 500/550 Integration Package v2.3.0 supports the integration of Clarity LIMS to Illumina NextSeq 500 and 550 sequencing systems.

The integration allows for automated tracking of an Illumina sequencing run in Clarity LIMS, which includes tracking instrument run status, generating run report, and capturing and parsing run statistics. In addition, this integration provides automated generation of a sample sheet file for use with bcl2fastq2 v2.20.0 analysis software.

This document describes the integration between Clarity LIMS and the NextSeq system. It includes information about protocols and automations, configuration options, installed components, and rules and constraints.

For instructions on user interaction for each step, validating and troubleshooting the NextSeq 500/550 Integration Package, refer to NextSeq 500/550 Integration v2.3.0 User Interaction, Validation and Troubleshooting.

Prerequisites and Assumptions

It is assumed that samples enter the NextSeq 500/550 Sequencing v1.1 workflow as normalized libraries and have reagent labels attached.

That is, before they are assigned to the workflow:

Samples have been accessioned into Clarity LIMS.
Samples have been run through QC and library prep.
Samples have been normalized, and the value is captured in a field called Normalized Molarity (nM).

For more information on sample accessioning, refer to Sample Accessioning and Upload and Modify Samples in the Getting Started section of the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

You can assign samples to workflows automatically, using a routing script, or manually — from the Projects & Samples dashboard. Refer to Assign and Process Samples in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

Workflows, Protocols, and Steps

NextSeq Integration Package v2.3.0 includes the NextSeq 500/550 Sequencing v1.1 workflow, which contains a single protocol of the same name.

The NextSeq 500/550 Sequencing v1.1 protocol includes the following steps:

Library Pooling (NextSeq 500/550 v1.1)
Denature & Dilute (NextSeq 500/550 v1.1)
NextSeq 500/550 Run (NextSeq 500/550 v1.1)

Step 1: Library Pooling (NextSeq 500/550 v1.1)

The Library Pooling (NextSeq 500/550 v1.1) step is derived from the Library Pooling v1.0 master step. Libraries are placed into pools manually.

Set Next Step - Advance Automation

This automation is automatically triggered on exit of the Record Details screen. The automation advances samples to the next step in the protocol.

The default command line is as follows.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"

Master Step Fields

This field is configured on the Library Pooling (NextSeq 500/550 v1.1) step and displays on the Record Details screen at run time.

The following table shows field configuration details.

Library Pooling (NextSeq 500/550 v1.1) Master Step Field Configuration

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-down Items

Comment

Multiline Text

Global Fields

The following table lists the global custom fields configured to display on the Queue and Ice Bucket screens of the Library Pooling (NextSeq 500/550 v1.1) step. Most of these fields show in the expanded view only.

Global Custom Field Configuration (Submitted Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Dropdown Items

Application

Text Dropdown

Custom Entries

Presets

TruSeq mRNA sequencing
TruSeq DNA sequencing (large genome de novo)
TruSeq DNA sequencing (large genome re-seq)
TruSeq DNA sequencing (small genome de novo)
TruSeq DNA sequencing (small genome re-seq)
Nextera DNA sequencing
TruSeq Custom Amplicon sequencing
ChIP-sequencing
Exome sequencing
Mate pair sequencing
Small RNA sequencing

Pooling

Text Dropdown

Custom Entries

Presets

Read Length

Text

Sequencing Coverage

Text

Sequencing Method

Text Dropdown

Custom Entries

Presets

Single Read
Paired End Read
Indexed Single read
Indexed Paired End Read

Global Custom Field Configuration (Derived Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Dropdown Items

Normalized Molarity (nM)

Numeric

Decimal places displayed = 2

Step 2: Denature and Dilute (NextSeq 500/550 v1.1)

In this step, pooled libraries are denatured and diluted and placed into the reagent cartridge that is loaded into the NextSeq instrument.

Generate bcl2fastq2 NextSeq SampleSheet Automation

This automation is triggered by a button on the Record Details screen.

This automation generates the sample sheet and attaches it to the step. For details, see the following section on sample sheet generation.

The default command line is as follows.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {processURI:v2} -u {username} -p {password} \
script:driver_file_generator \
-t /opt/gls/clarity/extensions/conf/driverfiletemplates/{udf:Samplesheet Template} \
-o {compoundOutputFileLuid1}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid1} \
-l {compoundOutputFileLuid2}"

Set Next Step - Advance Automation

This automation is automatically triggered on exit of the Record Details screen.

This automation advances samples to the next step in the protocol.

The default command line is as follows.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid3}"

Master Step Fields

There are 10 fields configured on the Denature and Dilute (NextSeq 500/550 v1.0) step. At run time, these fields display on the Record Details screen, in the Step Data table. The fields are manually populated. Their values are used to generate the sample sheet.

The following table lists field configuration details.

Denature and Dilute (NextSeq 500/550 v1.1) Master Step Field Configuration

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Adapter

Text

Adapter Read 2

Text

Experiment Name

Text

Mask Adapter

Text

Mask Adapter Read 2

Text

Read 1 Cycles

Numeric Dropdown

Required Field
Custom Entries

Presets
- 251 (Default)
- 151
- 101
- 76
- 51
Range = 0–1000
Decimal places displayed = 0

Read 2 Cycles

Numeric Dropdown

Custom Entries

Presets
- 251 (Default)
- 151
- 101
- 76
- 51
Range = 0–1000
Decimal places displayed = 0

SampleSheet Template

Text Dropdown

Presets
- BCL2FASTQ_Reverse_Complement_Samplesheet.csv (default)
- BCL2FASTQ_Samplesheet.csv

Workflow

Text Dropdown

Required Field

Presets
- Assembly
- Custom Amplicon
- Enrichment
- GenerateFASTQ
- LibraryQC
- Metagenomics
- PCR Amplicon
- Resequencing

Groups of Defaults

Resequencing

Read 1 Cycles = 251
Workflow = Resequencing

Custom Amplicon

Read 1 Cycles = 251
Workflow = Custom Amplicon

PCR Amplicon

Read 1 Cycles = 251
Workflow = PCR Amplicon

Enrichment

Read 1 Cycles = 251
Workflow = Enrichment

Library QC

Read 1 Cycles = 251
Workflow = Library QC

Metagenomics

Read 1 Cycles = 251
Workflow = Metagenomics

GenerateFastQ

Read 1 Cycles = 251
Workflow = GenerateFastQ

Assembly

Read 1 Cycles = 251
Workflow = Assembly

Global Fields

The following table lists the global fields that are configured to display on the Queue, Ice Bucket, and Record Details screens of the Denature and Dilute (NextSeq 500/550 v1.1) step.

Global Custom Field Configuration (Submitted Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Read Length

ℹ️ Displays on Queue & Ice Bucket screens

Text

Sequencing Method

ℹ️ Displays on Queue & Ice Bucket screens

Text Dropdown

Custom Entries

Presets
- Single Read
- Paired End Read
- Indexed Single Read
- Indexed Paired End Read

Global Custom Field Configuration (Derived Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Final Loading Concentration

ℹ️ Displays on Record Details screen

Numeric Dropdown

Required Field
Custom Entries

Presets
- 225
- 400
Decimal places displayed = 0

Step File Placeholders

Placeholders for the following files are configured on the Record Details screen of the Denature and Dilute (NextSeq 500/550 v1.1) step

Lab Tracking Form

Manually uploaded
This form in Clarity LIMS allows for manually attaching a lab-specific tracking form to the step.

bcl2fastq SampleSheet

Automatically attached
This CSV file is automatically generated by Clarity LIMS for use with the bcl2fastq2 v2.20.0 analysis software. It can be opened as a text file or as an MS Excel spreadsheet.

bcl2fastq SampleSheet Generation Log

Automatically attached
Automatically generated by Clarity LIMS, this log file captures any errors that Clarity LIMS can encounter when generating the sample sheet.

Log File

Automatically attached
Automatically generated by Clarity LIMS, this log file captures the status of the EvaluateDynamicExpression script that is launched by the Set Next Step - Advance automation.

Step 3: NextSeq 500/550 Run (NextSeq 500/550 v1.1)

In this step, pooled samples are sequenced on the NextSeq 500/550 instrument and the run metrics are recorded in Clarity LIMS.

Set Next Step - Advance Automation

This automation is automatically triggered on exit of the Record Details screen. The automation advances samples to the next step in the protocol.

The default command line is as follows.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid5}"

Master Step Fields

There are 16 fields configured on the NextSeq 500/550 Run (NextSeq 500/550 v1.1) step. These fields display on the Record Details screen at run time. Some of the field values must be completed manually, and the remaining fields are automatically populated at the end of the run.

The following table lists field configuration details.

NextSeq 500/550 Run (NextSeq 500/550 v1.1) Master Step Field Configuration

Field Name

Field Type

Field Constraints/Options

Preset Value/Additional Options and Drop-down Items

Chemistry

Text

Read Only

Comment

Multiline Text

Experiment Name

Text

Read Only

Finish Date

Date

Read Only

Flow Cell ID

Text

Read Only

Index 1 Read Cycles

Numeric

Read Only

Decimal places displayed = 0

Index 2 Read Cycles

Numeric

Read Only

Decimal places displayed = 0

Output Folder

Text

Read Only

PR2 Bottle ID

Text

Read Only

Read 1 Cycles

Numeric

Read Only

Decimal places displayed = 0

Read 2 Cycles

Numeric

Read Only

Decimal places displayed = 0

Reagent Cartridge ID

Text

Read Only

Run ID

Text

Read Only

Run Type

Text

Read Only

Status

Text

Read Only

Workflow

Text

Read Only

Global Fields

There are several sample and measurement global fields configured to display on the Record Details screen of the NextSeq 500/550 Run (NextSeq 500/550 v1.1) step. These fields are populated at the end of the sequencing run.

For more information, see the Sequencing Results Parsing section below.

Step File Placeholders

Placeholders for the following files are configured on the Record Details screen of the NextSeq 500/550 Run (NextSeq 500/550 v1.1) step.

Illumina Run Report (automatically attached)
Link to Run Folder (automatically attached)
Run Parameters (automatically attached)
Run Info (automatically attached)
Lab Tracking Form (manually uploaded)
Log File (automatically attached)

Sample Sheet Generation

Sample sheet generation occurs on the step before the sequencing run Denature and Dilute (NextSeq 500/550 v1.1) step. Samples are placed on the container to be loaded in the instrument. The default configuration provides the Generate bcl2fastq2 NextSeq Samplesheet automation.

The Generate bcl2fastq2 NextSeq Samplesheet automation uses the Template File Generator (DriverFileGenerator.jar) and a template file to generate a CSV format file for use with bcl2fastq2 v2.20.0 analysis software. The sample sheet content is determined by the fields that display on the Record Details screen of the step (in the Step Data table) and the values entered into the fields. Templates can be customized to create the sample sheet. If additional columns are required by the lab, then they can be inserted.

Sequencing Results Parsing

The NextSeq 500/550 Run (NextSeq 500/550 v1.1) step records information for the flow cell lanes and generates a report summarizing the results. In addition, run parameters, run info, and a link to the run folder are automatically captured.

Generated and Captured Files

The following table lists the run information files, reports, placeholders, and links that Clarity LIMS automatically generates or capture during a sequencing run.

Run Information Generated or Captured by NextSeq 500/550 Run (NextSeq 500/550 v1.1) Step

Item

Description

Run Info Run Parameters

These XML files are captured automatically by Clarity LIMS from the instrument run folder. They include the key run parameters, many of which are parsed out into key step global custom fields.

Link to Run Folder

Automatically generated by Clarity LIMS, and is a link to the network run folder where the data that was captured from the instrument during the run is stored.

Illumina Run Report

Automatically generated by Clarity LIMS, this report provides key information about the run and the samples on the flow cell.
Information includes the flow cell ID, run directory location, and primary analysis metrics for the instrument, summarized per flow cell lane for the entire run, and individual reads if there are paired-end runs.
These metrics are compared against the instrument per lane averages, calculated using metrics from the last 5 sequencing runs. Any values outside of 1 standard deviation are highlighted.

Lab Tracking Form

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

Metadata

The following list includes the metadata that Clarity LIMS automatically captures from the Illumina sequencing software as part of a sequencing run. This information is gathered from various run result files and events.

Chemistry
Experiment Name – entered in software
Finish Date — Run completion date
Flow Cell ID
Index 1 Read Cycles — Configured Index 1 length
Index 2 Read Cycles — Configured Index 2 length
Output Folder — Run folder root
PR2 Bottle ID
Reagent Cartridge ID
Read 1 Cycles - Configured Read 1 cycle
Read 2 Cycles - Configured Read 2 cycle
Run ID — The unique run ID
Run Type
Status — Displays the completed vs configured aggregated (i.e., Read 1 and Read 2) read cycles. Example: Cycle 10 of 100.
Workflow

If the End Run event contains a date in the format YYYY-MM-DD, Finish Date is set to the date in the event file. If the End Run event does not contain a date or the date is in the wrong format, Finish Date is set to the date when the event file is processed.

Primary Analysis Metrics

The following table lists the Real-Time Analysis v2 (RTA2) primary analysis metrics that Clarity LIMS automatically captures and records, per read, for samples in each flow cell lane. These metrics are captured after run completion and are stored as global custom fields in the Record Details screen Sample Details table. Per read and per lane metrics are viewable by expanding the output.

RTA Primary Analysis Metrics Captured by NextSeq 500/550 Run (NextSeq 500/550 v1.0) Step

Per Read Clarity LIMS Field Name (stored on derived sample/analyte input to the step)

Per Lane Clarity LIMS Field Name (stored in measurement placeholders in Record Details screens Sample Details table)

% Aligned R1

% Aligned R2

% Bases >=Q30 R1

% Bases >=Q30 R2

% Error Rate R1

% Error Rate R2

% Phasing R1

% Phasing R2

% Prephasing R1

% Prephasing R2

%PF R1

%PF R2

Cluster Density (K/mm^2) R1

Cluster Density (K/mm^2) R2

Intensity Cycle 1 R1

Intensity Cycle 1 R2

Reads PF (M) R1

Reads PF (M) R2

Yield PF (Gb) R1

Yield PF (Gb) R2

The sequencing service runs on the Clarity LIMS server. The service detects event files that the instrument software (RTA2) produces as the run progresses, which tells the service where to find the run data. As the run data is written out and the End Run event is detected, the data is matched to the step. This matching is based on the reagent cartridge ID that was entered/scanned in the Denature and Dilute (NextSeq 500/550 v1.1) step. Read-only field values on the Record Details screen are populated accordingly. When finished processing the end run event and updating the fields in Clarity LIMS, the sequencing service generates the report and attaches it to the step.

Components Installed

This integration requires installation of the Illumina Preset Protocols (IPP). For details, refer to NextSeq 500/550 Integration v2.3.0 Release Notes.

Scripts and Files Installed

The following table lists the scripts and files installed in the Illumina NextSeq 500/550 Integration Package v2.3.0 RPM.

Illumina NextSeq 500/550 Integration Package v2.3.0 Scripts and Files Installed

Files Installed

Location

Description

configure_extensions_nextseq_sequencingservice.sh

/opt/gls/clarity/config/

Script that installs the service properties in the database.

log4j2.xml

/opt/gls/clarity/extensions/Illumina_NextSeq/v2/SequencingService/conf

File containing the settings for the sequencing jar logging.

nextseq-sequencing.jar

/opt/gls/clarity/extensions/Illumina_NextSeq/v2/SequencingService

Jar file containing API-based Clarity LIMS extensions used for capturing run results and report generation.

InterOp libraries

opt/gls/clarity/extensions/Illumina_NextSeq/v2/lib

Shared library for parsing InterOp data files.

Installed from IPP

BCL2FASTQ_Reverse_Complement_Samplesheet.csv
BCL2FASTQ_Samplesheet.csv

/opt/gls/clarity/extensions/conf/driverfiletemplates

Template file used for file generation. In this integration, the reverse complement template is used by default.

Properties Installed

The following table lists the properties installed with Illumina NextSeq 500/550 Integration Package v2.3.0.

Additional properties, each with the 99 suffix appended to their name, are also installed and intended for use by the Clarity LIMS Support team in automated validation tests. Those properties are not listed in the table.

ℹ️ Sequencing runs are matched using the reagent cartridge ID and the sequencing steps base name. The base name is NextSeq 500/550 Run (NextSeq 500/550 v1.1). Do not change the base name. The name is expected by the sequencing service that captures instrument run results. The base name is stored in the sequenceProcessBaseName property. If this name is changed without the property being updated, the 'reagent cartridge ID <-> sequencing step base name' matching system fails. If necessary, modify the step name by editing or adding text after the base name portion, as it is not used in the matching system. For example, change NextSeq 500/550 Run (NextSeq 500/550 v1.1) to NextSeq 500/550 Run (NextSeq 500/550 v1.1) v2.

ℹ️ Changes on nextseq.v2.seqservice.sequenceProcessBaseName property take effect upon updates and do not require restart of the integration service. For all remaining properties, integration service has to be restarted for property changes to take effect.

Properties Installed with the Illumina NextSeq 500/550 Integration Package

Property

Description

Default Value

nextseq.v2.seqservice.sequenceProcessBaseName

ℹ️ Installed from the IPP

Sequencing process type / master step base display name. Partial matching is used to look up the process type / master step.

NextSeq 500/550 Run (NextSeq 500/550 v1.1)

nextseq.v2.seqservice.eventFileDirectory.1

A network location monitored for event files (e.g., /mnt/illumina/gls_events/)

/mnt/gls_events

nextseq.v2.seqservice.netPathPrefixSearch.1¹

The network directory prefix contained in the event file - most likely in Windows format.

\\nas\network\run_data

nextseq.v2.seqservice.netPathPrefixReplace.1

The mapped network directory mount name on the server used to access the run data directory (e.g., /mnt/network/data)

/mnt/run_data

nextseq.v2.seqservice.eventFileDirectorySuffixes

A list of eventFileDirectory path entries to monitor for event files. The value is one or more comma-separated integers.

ℹ️ Configured on install to point to 1.

nextseq.v2.seqservice.netPathPrefixSearchReplaceSuffixes

A list of netPathPrefix search and replace entries for transforming Windows to Linux network paths. The value is one or more comma-separated integers.

ℹ️ Configured on install to point to 1.

nextseq.v2.seqservice.runReportViewsVersion

The current version of the Run Report views in the database. The value 0 represents the state before the views are created. This property is automatically updated by the run report.

nextseq.v2.seqservice.ignoreUnmatchedContainerIds

A flag indicating if event files that cannot be matched to reagent cartridges in Clarity LIMS should be archived after a certain time (true), or continually reprocessed (false).

false

ℹ️ To prevent the gls_events file directory from becoming cluttered, it is recommended that the value of this property is set to true.

nextseq.v2.seqservice.ignoreUnmatchedContainerIdsWaitDays

The number of days between when the event is created and the event file is archived.

nextseq.v2.seqservice.synchronizationPeriod

Invocation period in seconds.

¹ It is possible to configure support for multiple, identical seqservice.netPathPrefixSearch property values.

Reagent Categories/Label Groups Installed

Reagent categories/label groups are installed with the IPP workflow configuration slices.

The NextSeq Reagent Kit is included in the NextSeq Integration.

Control Types Installed

The PhiX v3 control type is included in the NextSeq Integration.

Container Types Installed

The NextSeq Reagent Cartridge container type is included in the NextSeq Integration.

All one-dimensional container types with both numeric rows and numeric columns are supported.

Instrument Integration

To make sure that the Illumina instrument warranty remains valid, the instrument integration must be performed and maintained by the Clarity LIMS Support team. To perform this integration, the Support team requires remote access to the instrument while it is idle.

To configure the Illumina instrument for use with the Illumina NextSeq Integration, the Support team:

Creates a directory on the local computer to hold the batch files. These batch files write event files to the network attached storage (NAS) shares.
Creates a directory on the NAS to hold the event files.
Modifies Illumina software configuration files to call the batch files that create the event files.
Updates sequencing service default properties to match the specifics of the installation.

Rules and Constraints

This integration operates with the following constraints:

The reagent cartridge ID must be unique. Avoid multiple reagent cartridge containers in the system with identical names.
The reagent cartridge ID must be scanned as the reagent cartridge Container Name on the Denature and Dilute (NextSeq 500/550 v1.1) step.

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