Run Planning

Planned runs let team members create and manage runs in ElemBio Cloud for use on any connected AVITI System. A team member can plan the run in ElemBio Cloud, then select it during run setup.

You can only edit or delete planned runs through ElemBio Cloud.

Planned Runs

The Planned Runs table displays saved configuration information for planned runs. Buttons let you search and filter the runs. Planned runs appear as in-use during run setup and before priming begins.

After an instrument starts processing a planned run, the following rules apply:

• If you discard a planned run before priming, the in-use status disappears. The run becomes available for selection on an instrument.
• After priming, the run moves from Planned Runs to the Active Runs and All Runs pages.
• If you discard the run or the run fails after priming, you cannot make it available again as a planned run. Instead, you must recreate the planned run.

Add a Planned Run

1. On the Planned Runs page, select Plan a Run.

2. Enter a unique name for the run.

3. If you have prepared a run manifest, upload it:

   1. Select Browse, and then browse to the run manifest file.
   2. Select the run manifest file, and then select OK.

4. Enter an optional description that represents the run.

5. Select a Library Type: Adept, Elevate, or Third Party.

6. If you are using an Adept or Elevate library, select a Library Structure.

   • Circular: Sequences libraries that complete circularization before loading.
   • Linear: Sequences libraries prepared for on-instrument circularization.

7. In the Sequencing Kit drop-down menu, select your kit.

8. If you are using an Adept or third-party library, select a Low-Diversity High-Multiplex option.

   • Yes: Sequence low-diversity high-multiplex libraries. Selecting Yes requires at least 4 cycles for Index 1.
   • No: Sequence other libraries.

9. If you are using the Individually Addressable Lanes add-on, select the number of libraries.

10. In the Cycles fields, enter the number of cycles to perform in each read.

    • To skip a read, enter 0.
    • For bioinformatics purposes, add one cycle to Read 1 and Read 2. For example, enter 151 in the Read 1 field to perform 150 cycles in Read 1.
    • See the following table for minimum cycle values for each read and the maximum number of total cycles. Aside from these limitations, you can distribute the available cycles among reads as necessary.

    Workflow	Kit	Index 1 Minimum	Index 2 Minimum	Read 1 Minimum	Read 2 Minimum	Maximum Total Cycles
    Adept or Third Party	2 x 75	0	0	5	0	184
    Adept or Third Party	2 x 150	0	0	5	0	334
    Adept or Third Party	2 x 300	0	0	5	0	634
    Elevate	2 x 75	4	0	5	0	184
    Elevate	2 x 150	4	0	5	0	334
    Elevate	2 x 300	4	0	5	0	634

11. Select Save Run.

    ElemBio Cloud saves the run, which appears in the Planned Runs table.

Edit a Planned Run

1. On the Planned Runs page, locate the run you want to edit.
2. In the Actions column, select More, and then select Edit.
3. Update the run information as needed.
4. Select Save Run.

Delete a Planned Run

1. On the Planned Runs page, locate the run you want to delete.
2. In the Actions column, select More, and then select Delete.
3. When prompted, enter the name of the planned run.
4. Select Delete to immediately remove the run.

Run Manifest Validation

When you add or edit a planned run, ElemBio Cloud validates any attached run manifest. Validation ensures the run manifest is compatible with the planned run setup. If the run manifest contains mistakes or invalid data, ElemBio Cloud displays a list of errors and warnings.

You can save a planned run with warnings, but not errors. Before proceeding, resolve the errors and reupload the run manifest. For help setting up a run manifest, see the Run Manifest Documentation.