The NextSeq 500/550 Integration v2.5.0 integration package requires the NextSeq 500/550 v1.3 workflow available from IPP v2.10. If you do not want to upgrade through the IPP, you can manually upgrade the workflow configuration from NextSeq 500/550 v1.2 workflow to v1.3 workflow by following instructions in this guide to generate samplesheet compatible with LRM v4.0.
To support the generation of LRM v4.0-compatible samplesheet, you must modify the Denature and Dilute step, and replacement of template files.
Automation
From Configuration, select the Automation tab.
Rename the Generate bcl2fastq2 NextSeq Samplesheet automation to Generate NextSeq Samplesheet.
The default command line for the automation remains unchanged.
Master Step Fields
From Configuration, select the Custom Fields tab.
Select the Denature and Dilute Master Step.
Add the following master step fields:
Group of Defaults
From Configuration, select the Custom Fields tab.
Select the Denature and Dilute Master Step.
Add the following Group of Defaults:
Step File Placeholders
From Configuration, select the Lab Work tab.
Select the Denature and Dilute Master Step.
Rename the following Step File Placeholders under Record Details milestone:
Replace the following template files at /opt/gls/clarity/extensions/conf/driverfiletemplates/:
BCL2FASTQ_Reverse_Complement_Samplesheet.csv with NextSeq_ReverseComplement_Samplesheet.csv
BCL2FASTQ_Samplesheet.csv with NextSeq_Samplesheet.csv
Contact Illumina Support to replace the files if required.
Field Constraints/Options
Preset Values/Additional Options and Drop-Down Items
Comment
Multiline Text
Genome Folder
Text
Manifest
Text
Samplesheet Template
Text Dropdown
Required Field
Presets
NextSeq_Samplesheet.csv
NextSeq_ReverseComplement_Samplesheet.csv
Taxonomy Database
Text
Remove the following master step fields:
Adapter
Adapter Read 2
Mask Adapter
Mask Adapter Read 2
SampleSheet Template
Update the following master step fields:
Field Name
Changes Required
Screenshot
Experiment Name
Update Required Field to Yes
Workflow
Update Dropdown presets to
Assembly
DNA Amplicon
Screenshot
RNA Fusion
Read 1 Cycles = 251
Workflow = RNA Fusion
Small RNA
Read 1 Cycles = 251
Workflow = Small RNA
Update the following Group of Defaults:
Group of Defaults
Changes Required
Screenshot
Custom Amplicon
Rename to DNA Amplicon
Update Workflow field to DNA Amplicon
Enrichment
Rename to DNA Enrichment
Update Workflow field to DNA Enrichment
Generate FASTQ
Rename to GenerateFASTQ
from bcl2fastq SampleSheet Generation Log to Samplesheet Generation Log
Field Name
Group of Defaults
Field Type
Details
GenerateFASTQ
Library QC
16S Metagenomics
PCR Amplicon
Resequencing
RNA Fusion
Small RNA
Library QC
Update Workflow field to Library QC
Metagenomics
Rename to 16S Metagenomics
Update Workflow field to 16S Metagenomics
