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.

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

• BCL2FASTQ_Samplesheet.csv with NextSeq_Samplesheet.csv