Manual denaturation of libraries on the NextSeq 1000/2000

Manual denature and dilution is recommended for low concentration libraries that are unable to meet the recommended loading concentration and volume as stated in the NextSeq 1000 and NextSeq 2000 Product Documentation.

The NextSeq 1000/2000 Denature and Dilute Libraries Guide contains:

• Recommended final loading concentrations (what is loaded into the cartridge after denaturation and dilution) and corresponding starting library concentrations.

• Instructions for Manual Denature and Dilution

To optimize loading for libraries that have not been validated by Illumina:

• For XLEAP-SBS reagents, see Knowledge Base Article: NextSeq 1000/2000 Loading Optimization for XLEAP-SBS

• For Standard SBS reagents, see Knowledge Base Article: NextSeq 1000/2000 Loading Optimization for Standard SBS

Run Setup for Manual Denature and Dilution

Onboard Denature and Dilution is enabled by default on the NextSeq 1000/2000. There are two methods to disable the onboard denaturation and dilution in the system.

Option 1: Set Denature and Dilute Preferences from Settings. This will change the default denature and dilution strategy for all runs. This is preferred if all runs on the system are to be manually denatured and diluted.

1. From the control software menu, select Settings.

2. Choose whether to automatically denature and dilute libraries onboard the instrument.

   • To disable denature and dilute libraries automatically onboard the instrument, uncheck the Denature and Dilute On Board checkbox.

Option 2: Confirm of Change Setting in Run Review Screen. If performing manual denature and dilute for a single run, modify the setting within the run review screen during the run setup.

1. From the Run Review screen, disable manual denature and dilution.

• Example:

  

The runparameters.xml file will indicate if denature and dilution were performed onboard or off instrument.

Run Parameters Setting	Strategy
<SkipObdd>false</SkipObdd>	On Board Denature and Dilution preformed (default)
<SkipObdd>true</SkipObdd>	On Board Denature and Dilution omitted

For any feedback or questions regarding this article (Illumina Knowledge Article #3741), contact Illumina Technical Support [e-mail].