How to select custom recipes on the NextSeq 500/550 in NextSeq Control Software (NCS) 4.0.X

Note: "Custom recipes" refers to files that change the standard chemistry and/or imaging steps in a sequencing run. The performance of custom sequencing recipes is not guaranteed, and custom recipes are not able to be provided in all cases or for all requests.

• In order to use custom recipes, runs must be setup in manual mode.

• In NCS 4.0.X, if a custom recipe is to be used, the option to select the custom recipe will occur only after the reagent cartridge is loaded (not during the run setup page earlier).

• By this point, a new flow cell, buffer cartridge, and reagent cartridge will need to be recognized in order to test the custom recipe.

  1. Make sure the custom recipe is in the correct location.* Custom Recipes Location (C:\Program Files\Illumina\NextSeq Control Software\Recipe\Custom)

• Note:

  • All custom recipes must be located in one of the following locations: - C:\Program Files\Illumina\NextSeq Control Software\Recipe\Custom\High - C:\Program Files\Illumina\NextSeq Control Software\Recipe\Custom\Mid

  • Custom recipes must NOT be located in these following locations: - C:\Program Files\Illumina\NextSeq Control Software\Recipe\High - C:\Program Files\Illumina\NextSeq Control Software\Recipe\Mid.

  • If the other file paths are used, the custom recipes will not show up in the selection box during the consumable loading step.

1. Make sure custom recipes are enabled in 'System Customization' (if not selected, the Custom Recipe option will not appear during run setup).1. From the NextSeq Control Software (NCS), select Manage Instrument.

2. Select System Customization.

3. Select Enable Custom Recipes.

4. Select Save.

1. Proceed through run setup.1. Select Experiment.

2. Select Sequence.

3. Select Manual Mode > Next.

• Note: If attempting to use Local Run Manager mode, the option to select a custom recipe will not be available.

1. Enter the desired run parameters.

• ie, Run name, Read length, Custom primers, etc.

• Note: When using a custom recipe, enter the desired number of cycles for run setup. Dark cycles (chemistry cycles that are not imaged) do not need to be included in the run length as they will be implemented by using the custom recipe.

  • For example: If the desired run setup includes 10 dark cycles at the beginning of the first index, with a desired index length of 10 cycles, and desired read lengths of 151 cycles, the run setup must be entered as 151 | 10 |10 |151, as the dark cycles will be accounted for through the custom recipe.

1. Load the reagent and buffer cartridges and select Next.

2. Load the flow cell.

3. Select the custom recipe from the drop down menu > Select Next.

4. Review the run setup and select Next to proceed with pre-run checks and begin the sequencing run.

The image below indicates all consumables need to be loaded before having access to selecting custom recipe.

For any feedback or questions regarding this article (Illumina Knowledge Article #2138), contact Illumina Technical Support [e-mail].