Manual Upgrade

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.

Generate NextSeq 500/550 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.

Modify Denature and Dilute Step

Automation

1. From Configuration, select the Automation tab.

2. Rename the Generate bcl2fastq2 NextSeq Samplesheet automation to Generate NextSeq Samplesheet.

The default command line for the automation remains unchanged.

Master Step Fields

1. From Configuration, select the Custom Fields tab.

2. Select the Denature and Dilute Master Step.

3. Add the following master step fields:

   Field Name	Field Type	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

4. Remove the following master step fields:

   • Adapter

   • Adapter Read 2

   • Mask Adapter

   • Mask Adapter Read 2

   • SampleSheet Template

5. 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 DNA Enrichment GenerateFASTQ Library QC 16S Metagenomics PCR Amplicon Resequencing RNA Fusion Small RNA

Group of Defaults

1. From Configuration, select the Custom Fields tab.

2. Select the Denature and Dilute Master Step.

3. Add the following Group of Defaults:

   Group of Defaults	Details	Screenshot
   RNA Fusion	Read 1 Cycles = 251 Workflow = RNA Fusion
   Small RNA	Read 1 Cycles = 251 Workflow = Small RNA

4. 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
   Library QC	Update Workflow field to Library QC
   Metagenomics	Rename to 16S Metagenomics Update Workflow field to 16S Metagenomics

Step File Placeholders

1. From Configuration, select the Lab Work tab.

2. Select the Denature and Dilute Master Step.

3. Rename the following Step File Placeholders under Record Details milestone:

   • from bcl2fastq SampleSheet to Samplesheet

   • from bcl2fastq SampleSheet Generation Log to Samplesheet Generation Log

Replace Template Files

Replace the following template files at /opt/gls/clarity/extensions/conf/driverfiletemplates/:

• BCL2FASTQ_Reverse_Complement_Samplesheet.csv with NextSeq_ReverseComplement_Samplesheet.csv

2KB

NextSeq_ReverseComplement_Samplesheet.csv

• BCL2FASTQ_Samplesheet.csv with NextSeq_Samplesheet.csv

2KB

NextSeq_Samplesheet.csv

Contact Illumina Support to replace the files if required.