Plan Run Using Prep Tab

On the Plan Run page, click the Select Instrument drop-down arrow, and select a sequencing system, either MiniSeq or NextSeq.

In the Name field, enter a name for the sequencing run.

[Optional] In the Reagent Barcode field, enter the barcode ID of the reagent kit used for the run. Entering the barcode ID links the reagent kit to the run.

[Optional] Select Use Custom Primer options:

• R1 — Use custom primer for Read 1.

• R2 — Use custom primer for Read 2.

Select a read type, either Single Read or Paired End.

Enter the number of cycles for each read in the sequencing run:

• Read 1 Cycles — Enter a value up to 151 cycles.

• Read 2 Cycles — Enter a value up to 151 cycles. This value is typically the same number of cycles as Read 1.

Review the indexing scheme for the run. To make changes, override the defaults as follows.

1. Select the Override default indexing scheme checkbox.

2. Select an indexing scheme:

   • Single Index — Performs a run with 1 index read.

   • Dual Index — Performs a run with 2 index reads.

   • No Index — Performs a non-indexed run.

3. Enter the number of cycles for each index read*:

   • Index 1 Cycles — Enter the number of cycles required for the Index 1 (i7) primer.

   • Index 2 Cycles — Enter the number of cycles required for the Index 2 (i5) primer.

Make sure that a pool is present.

Select 1 of the following buttons to continue:

• Sequence — The run appears on the Planned Runs list with a status of Ready. The run becomes available from the control software of your sequencing system.

• Save and Continue Later — The run appears on the Planned Runs list with a status of Planning. When you are ready to sequence, select the checkbox for the run and select Sequence. The run then becomes available from the control software of your sequencing system.