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.

Run Progression

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

• During run setup and before priming begins, the status of a planned run appears as In Use.
• If you discard a planned run before priming, the In Use status disappears. The run becomes available again for selection on an instrument.
• After priming, the run moves from the Planned Runs table 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.

Compatibility

Planned runs only appear in the AVITI Operating Software (AVITI OS) if they are compatible with the AVITI System. Compatibility depends on the AVITI OS version and the available add-ons. When you add or edit a planned run, a statement at the bottom of the form identifies the run compatibility requirements.

The following table defines the compatibility requirements for different configurations of a planned run.

Planned Run Configuration	AVITI OS Requirement	Add-On Requirement
Two library pools	2.3.0+	Individually Addressable Lanes
Low-Diversity High-Multiplex with a 2 x 300 Cloudbreak™ sequencing kit and an Adept library	2.4.0+
Low-Diversity High-Multiplex with other kits or library types	2.5.0+
Cloudbreak Freestyle™ (CB Freestyle) sequencing kit	2.5.0+
High Density or Expert Mode HD	2.6.0+	Advanced Run Settings: Polony Density
Filter Mask	2.6.0+	Advanced Run Settings: Filter Mask
Custom Recipe	2.6.0+	Advanced Run Settings: Custom Recipes
Cloudbreak UltraQ™ (CB UltraQ) sequencing kit	2.6.0+

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 the CSV file.

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.

    Library Type	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. If you are using the Advanced Run Settings add-on, select Advanced Run Settings and proceed to Configure Advanced Run Settings.

    Planned runs that use an Advanced Run Setting are only available on instruments with the specific setting enabled.

12. Select Save Run.

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

Configure Advanced Run Settings

To plan a run that uses the Advanced Run Settings add-on, Element must first enable at least one setting for your organization. When you select a compatible kit in the Sequencing Kit drop-down menu, ElemBio Cloud enables the options for the available settings. For more information on the add-on and these settings, see Advanced Run Settings.

1. If you are using the Polony Density setting, select a Polony Density option.
   • Standard—Uses the standard read output.
   • High Density—Increases the read output.
2. If you are using the Filter Mask setting, enter a base mask to use for filtering.
   • Use the base mask format.
   • If you do not use the Filter Mask setting, the default filter mask is R1:Y15N*-R2:Y15N*.
3. If you are using the Custom Recipes setting, use the drop-down menu to select a recipe.
   • For a preloaded custom recipe, select the option for the recipe.
   • For other custom recipes, select Upload a custom recipe file, and then upload the .rec file provided by Element.
4. Select Next to proceed.

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.