Dark Cycle Sequencing
This section describes how to use dark cycle sequencing in the recipe.
Dark cycle sequencing is used to complete only the chemistry steps of a sequencing cycle. Check the Compatible Products page for your library prep kit on the Illumina Support Site to see if dark cycle sequencing is required.
Use the following steps for dark cycle sequencing.
| 1. | To request the appropriate recipe XML file for editing, contact Illumina Technical Support. |
| 2. | Edit the recipe XML file. |
| a. | Navigate to the <ReadDefinitions> section in the recipe file, and then identify the <ReadDefinition Name="Read 1"> and the <ReadDefinition Name="Read 2"> sections. |
| b. | In <ReadDefinition Name="Read 1">, add the following dark cycle step on a new line before <ImagingRef ImagingName="Cycle1ReadImaging"/> and after <ChemistryRef ChemistryName="FirstBase"/>: |
<ChemistryRef ChemistryName="CompleteCycleReuse"/>.
| c. | In <ReadDefinition Name="Read 2">, add the dark cycle step on a new line before <ImagingRef ImagingName="Cycle1ReadImaging"/> and after <ChemistryRef ChemistryName="FirstBase"/>. |
| 3. | Save the recipe XML file. |
The following is a sample recipe with the dark cycle step:
...
<ReadDefinitions>
<ReadDefinition Name="Read 1">
<CycleStepCollection Name="Cycle1" Cycles="1">
<ChemistryRef ChemistryName="FirstBase"/>
<ChemistryRef ChemistryName="CompleteCycleReuse"/>
<ImagingRef ImagingName="Cycle1Read1Imaging"/>
</CycleStepCollection>
<CycleStepCollection Name="CompleteCycle" Cycles="read1cycles-1">
<ChemistryRef ChemistryName="CompleteCycleReuse"/>
<ImagingRef ImagingName="CompleteCycleImaging" />
</CycleStepCollection>
</ReadDefinition>
...
<ReadDefinition Name="Read 2">
<CycleStepCollection Name="Cycle1" Cycles="1">
<ChemistryRef ChemistryName="FirstBase"/>
<ChemistryRef ChemistryName="CompleteCycleReuse"/>
<ImagingRef ImagingName="Cycle1Read4Imaging" />
</CycleStepCollection>
<CycleStepCollection Name="CompleteCycle" Cycles="read2cycles-1">
<ChemistryRef ChemistryName="CompleteCycleReuse"/>
<ImagingRef ImagingName="CompleteCycleImaging" />
</CycleStepCollection>
</ReadDefinition>
</ReadDefinitions>
...
