Manual Upgrade

This section describes the manual upgrade process from IPP v2.7 to IPP v2.8 to enable the changes described in Illumina Preset Protocols v2.8 Release Notes. If you do not want to upgrade the latest workflow through IPP, then update the workflow configuration manually using the following information.

The manual upgrade instructions for IPP v2.8 include the following information:

• Support for the new Illumina DNA/RNA UD Indexes Sets A–D.

• A sample sheet bug fix for the MiSeq v3.2 workflow.

• Updates to the sequencing instrument presets and routing scripts to remove the HiSeq series instruments and to support the new NextSeq 1000/2000 on-premise integration. For manual upgrade instructions for the NextSeq 1000/2000 Sequencing workflow, refer to NextSeq 1000/2000 Integration v2.5.0 Manual Upgrade.

• An update to the step output naming convention for Library Prep Validation.

  ⚠️ This modification supports generation of planned run using samples having duplicate names with different indexes for NextSeq 1000/2000 and NovaSeq X Series sequencers.

DNA/RNA UD Indexes

To support the new DNA/RNA UD indexes, you must upload the new label list files and add the label groups to steps within the protocols.

Upload Label List Files

Download the following label list files and upload them to Clarity LIMS as new label groups. For instructions, refer to Add and Configure Labels and Label Groups in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

Illumina DNA-RNA UD Indexes Set A B C D Tagmentation (MD5 = 99d5c7159677638ad1c67dfd07c7b675):

23KB

Illumina DNA-RNA UD Indexes Set A B C D Tagmentation-label-sheet.xlsx

Illumina DNA-RNA UD Indexes Set A Tagmentation (MD5 = 39952f3e644ab0889cb5a17ece76eb37):

12KB

Illumina DNA-RNA UD Indexes Set A Tagmentation-label-sheet.xlsx

Illumina DNA-RNA UD Indexes Set B Tagmentation (MD5 = d1ab38606a6af2837bf70a20faaad39a):

12KB

Illumina DNA-RNA UD Indexes Set B Tagmentation-label-sheet.xlsx

Illumina DNA-RNA UD Indexes Set C Tagmentation (MD5 = c562e964d1958cdf7900e2d50805a2a9):

12KB

Illumina DNA-RNA UD Indexes Set C Tagmentation-label-sheet.xlsx

Illumina DNA-RNA UD Indexes Set D Tagmentation (MD5 = 8dc20541d231c226784c43791ec7c6fb):

12KB

Illumina DNA-RNA UD Indexes Set D Tagmentation-label-sheet.xlsx

Illumina RNA UD Indexes Set A B C D Ligation (MD5 = f79e72899e02b546fc93b977546e83ae):

23KB

Illumina RNA UD Indexes Set A B C D Ligation-label-sheet.xlsx

Illumina RNA UD Indexes Set A Ligation (MD5 = 733f11e1462989d1f5a7c1e933214f71):

12KB

Illumina RNA UD Indexes Set A Ligation-label-sheet.xlsx

Illumina RNA UD Indexes Set B Ligation (MD5 = 0fda17945b89a12f0093bc01b5492519):

12KB

Illumina RNA UD Indexes Set B Ligation-label-sheet.xlsx

Illumina RNA UD Indexes Set C Ligation (MD5 = dd3dffc584d11987224bc7c968d2939b):

12KB

Illumina RNA UD Indexes Set C Ligation-label-sheet.xlsx

Illumina RNA UD Indexes Set D Ligation (MD5 = 47a067849c9b20eebe100e96156a4fdd):

12KB

Illumina RNA UD Indexes Set D Ligation-label-sheet.xlsx

Add Label Groups to Steps in Protocols

From the Add Labels tab of the Configuration page, add the following label groups for each protocol or master step in the table for workflows when upgrading from IPP v2.7 to IPP v2.8:

• Illumina DNA-RNA UD Indexes Set A B C D Tagmentation

• Illumina DNA-RNA UD Indexes Set A Tagmentation

• Illumina DNA-RNA UD Indexes Set B Tagmentation

• Illumina DNA-RNA UD Indexes Set C Tagmentation

• Illumina DNA-RNA UD Indexes Set D Tagmentation

Workflow	Protocol	Step
Illumina COVIDSeq Workflow v1.5	Library Prep (Illumina COVIDSeq Workflow v1.5)	Amplify Tagmented Amplicons (Illumina COVIDSeq Workflow v1.5)
Illumina DNA PCR-Free Library Prep Manual v1.0.2	Library Prep - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.2)	Ligate Indexes (Illumina DNA PCR-Free Library Prep Manual v1.0.2)
Illumina DNA PCR-Free Library Prep Manual v1.0.2	Library Prep - Thermal Cycler Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.2)	Ligate Indexes - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.2)
Illumina DNA Prep (M) Tagmentation v1.0.7	Library Prep (Illumina DNA Prep (M) Tagmentation v1.0.7)	Amplify Tagmented DNA (Illumina DNA Prep (M) Tagmentation v1.0.7)
Illumina DNA Prep with Enrichment (S) Tagmentation v1.1	Not applicable	Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.1)
Illumina RNA Prep with Enrichment (L) Tagmentation v1.0	Library Prep (Illumina RNA Prep with Enrichment (L) Tagmentation v1.1)	Amplify Tagmented cDNA (Illumina RNA Prep with Enrichment (L) Tagmentation v1.1)

From the Add Labels tab of the Configuration page, add the following label groups for each protocol or master step in the table:

• Illumina RNA UD Indexes Set A B C D Ligation

• Illumina RNA UD Indexes Set A Ligation

• Illumina RNA UD Indexes Set B Ligation

• Illumina RNA UD Indexes Set C Ligation

• Illumina RNA UD Indexes Set D Ligation

Workflow	Protocol	Step
Illumina Stranded mRNA Prep Ligation v1.0	Library Prep (Illumina Stranded mRNA Prep Ligation v1.0)	Amplify Library (Illumina Stranded mRNA Prep Ligation v1.0)
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.0	Library Prep (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)	Amplify Library (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

ℹ️ Similar changes are required if you wish to enable support of the new DNA/RNA UD indexes on older workflows from earlier IPP versions (v2.6 and below).

MiSeq v3.2 Sample Sheet Bug Fix

Replace the MiSeqSamplesheetv3.csv file at

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

ℹ️ Contact Illumina Support to replace the file if required.

Update Sequencing Instrument Presets

The following are obsolete and removed as options for the Sequencing Instrument derived sample custom field:

• HiSeq2500

• HiSeq3000/4000

• HiSeqX

A new option for the NextSeq 1000/2000 on-premise integration has been added. The preset options have been reordered as follows.

• MiSeq

• NextSeq

• NextSeq 1000/2000

• NextSeq 1000/2000 On-Prem

• NovaSeq 2.0

• NovaSeq 3.0

• NovaSeqDx

• NovaSeq X Series

Update Routing Scripts

The routing script needs to be updated to remove the routing options for obsolete instruments and to add a new option for the on-premise integration of the NextSeq 1000/2000. Modify the automation script as follows.

1. Remove the HiSeq instruments from the script:

   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'HiSeq2500' \
   --WORKFLOW 'HiSeq 2500 Sequencing v1.0' \
   --STEP 'Library Pooling (HiSeq 2500 v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \
   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'HiSeq3000/4000' \
   --WORKFLOW 'HiSeq 3000/4000 Sequencing v1.0' \
   --STEP 'Library Pooling (HiSeq 3000/4000 v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \
   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'HiSeqX' \
   --WORKFLOW 'HiSeq X Sequencing v1.0' \
   --STEP 'Library Pooling (HiSeq X v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \

2. Add the on-premise NextSeq 1000/2000 instrument to the script:

   \
   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \
   --WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \
   --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS'"

3. [Optional] If you are using the NextSeq 1000/2000 Sequencing workflow v2.4, update the workflow version in the script:

   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'NextSeq 1000/2000' \
   --WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \
   --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \

Update Library Prep Validation Step Output Naming Convention

1. Select the Configuration tab, and then select the Lab Work tab.

2. Under Master Steps, select the Library Prep Validation master step.

3. Navigate to the Step Type pane and update Naming Convention to

   {SubmittedSampleName}_{OutputItemLIMSID}