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 .
An update to the step output naming convention for Library Prep Validation. {% hint style="danger" %} This modification supports generation of planned run using samples having duplicate names with different indexes for NextSeq 1000/2000 and NovaSeq X Series sequencers. {% endhint %}
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 () documentation.
Illumina DNA-RNA UD Indexes Set A B C D Tagmentation (MD5 = 99d5c7159677638ad1c67dfd07c7b675):
Illumina DNA-RNA UD Indexes Set A Tagmentation (MD5 = 39952f3e644ab0889cb5a17ece76eb37):
Illumina DNA-RNA UD Indexes Set B Tagmentation (MD5 = d1ab38606a6af2837bf70a20faaad39a):
Illumina DNA-RNA UD Indexes Set C Tagmentation (MD5 = c562e964d1958cdf7900e2d50805a2a9):
Illumina DNA-RNA UD Indexes Set D Tagmentation (MD5 = 8dc20541d231c226784c43791ec7c6fb):
Illumina RNA UD Indexes Set A B C D Ligation (MD5 = f79e72899e02b546fc93b977546e83ae):
Illumina RNA UD Indexes Set A Ligation (MD5 = 733f11e1462989d1f5a7c1e933214f71):
Illumina RNA UD Indexes Set B Ligation (MD5 = 0fda17945b89a12f0093bc01b5492519):
Illumina RNA UD Indexes Set C Ligation (MD5 = dd3dffc584d11987224bc7c968d2939b):
Illumina RNA UD Indexes Set D Ligation (MD5 = 47a067849c9b20eebe100e96156a4fdd):
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
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
MiSeq v3.2 Sample Sheet Bug Fix
Replace the MiSeqSamplesheetv3.csv file at
Update Sequencing Instrument Presets
The following are obsolete and removed as options for the Sequencing Instrument derived sample custom field:
A new option for the NextSeq 1000/2000 on-premise integration has been added. The preset options have been reordered as follows.
NextSeq 1000/2000 On-Prem
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.
Remove the HiSeq instruments from the script:
Add the on-premise NextSeq 1000/2000 instrument to the script:
[Optional] If you are using the NextSeq 1000/2000 Sequencing workflow v2.4, update the workflow version in the script:
Update Library Prep Validation Step Output Naming Convention
Select the Configuration tab, and then select the Lab Work tab.
Under Master Steps, select the Library Prep Validation master step.
Navigate to the Step Type pane and update Naming Convention to
