Run Planning for Sequencing

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. The Planned Runs table displays saved configuration information for planned runs. You can only edit or delete planned runs through ElemBio Cloud.

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 is removed and the run becomes available again for selection on 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 OS if they are compatible with the AVITI System. Compatibility depends on the AVITI OS version, AVITI System type, and 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 sequencing run.

Planned Run Configuration	Compatible AVITI OS Version	Compatible AVITI Systems	Add-On Requirement
Two library pools	2.3.0+	AVITI LT, AVITI, AVITI24	Individually Addressable Lanes
Low-Diversity High-Multiplex with a 2 x 300 Cloudbreak™ sequencing kit and an Adept library	2.4.0+	AVITI, AVITI24	No add-on required
Low-Diversity High-Multiplex with other kits or library types	2.5.0+	AVITI LT, AVITI, AVITI24	No add-on required
Cloudbreak Freestyle™ sequencing kit	2.5.0+	AVITI LT, AVITI, AVITI24	No add-on required
High Density or Expert Mode HD	2.6.0+	AVITI, AVITI24	Add-on required below AVITI OS v3.0.0
Filter Mask	2.6.0+	AVITI LT, AVITI, AVITI24	Advanced Run Settings: Filter Mask
Custom Recipe	2.6.0+	AVITI LT, AVITI, AVITI24	Add-on required below AVITI OS v3.0.0
Cloudbreak UltraQ™ sequencing kit	2.6.0+	AVITI, AVITI24	No add-on required
PMG Shift	3.0.0+	AVITI LT, AVITI, AVITI24	Advanced Run Settings: PMG Shift
Trinity™ sequencing kit	3.0.0+	AVITI, AVITI24	No add-on required
Cloudbreak 2 x 75 Low sequencing kit	3.1.0+	AVITI LT, AVITI, AVITI24	No add-on required

Add a Planned Run

Sequencing with Cloudbreak

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

2. Select Sequencing with Cloubreak.

3. Enter a unique name for the run.

4. If you have prepared a run manifest, upload the CSV file.

5. Enter an optional description that represents the run.

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

7. If you are using an Adept library, select a Library Structure.

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

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

9. 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.

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

11. 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

12. 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 feature enabled.

13. Select Save Run.

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

Sequencing with Trinity

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

2. Select Sequencing with Trinity.

3. Enter a unique name for the run.

4. If you have prepared a run manifest, upload the CSV file.

5. Enter an optional description that represents the run.

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

7. In the Panel drop-down menu, select your panel.

   • Twist for Element, Trinity Exome Workflow: For use with Twist Exome standard or fast hybridization protocols.
   • xGen Exome Kit for Trinity: For use with the IDT xGen Exome hybridization protocol.
   • Other: For use with custom panel.

8. 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
   Elevate	2 x 75	4	0	5	0	184
   Elevate	2 x 150	4	0	5	0	334

9. 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 feature enabled.

10. Select Save Run.

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

Configure Advanced Run Settings

At the bottom of the sequencing run planning form, Advanced Run Settings can be opened. When you select a kit in the Sequencing Kit drop-down menu, ElemBio Cloud enables the settings for the available features.

For more information about the features that require add-ons, see the compatibility table.

Polony Density

The Polony Density feature, also known as Expert Mode HD, relaxes certain quality filters to increase the total number of polonies in a run for increased read output. High Density is not available for AVITI LT Systems. To apply Expert Mode HD, select an option:

• Standard: Uses the standard read output (default option)
• High Density: Increases the read output.

Filter Mask

The Filter Mask feature modifies the cycles used for filtering, which is advantageous for certain applications. Applying the feature causes run output data and on-instrument run metrics to account for the filter mask. To apply a filter mask:

• Enter the filter mask in base mask format.
• If you do not use the Filter Mask feature, the default filter mask is R1:Y15N*-R2:Y15N*.

Custom Recipes

The Custom Recipe feature tailors a run execution in consultation with Element by enabling a custom recipe. A recipe governs the stages of a sequencing run, so custom recipes can impact specifications and significantly increase run times. To apply a custom recipe, use the drop-down menu in the planned run to select a recipe based on two options:

• Preloaded recipe: Select a recipe already loaded onto AVITI Systems, such as short insert and long insert custom recipes. Before using a preloaded recipe, contact Element Technical Support to ensure run compatibility. The following pre-loaded recipes are available:
  • Short insert recipe: If you are using Cloudbreak Freestyle chemistry and libraries with ≤ 100 bp DNA inserts, such as miRNA libraries, use the short insert recipe. The recipe is only compatible with 2 x 75 and 2 x 150 sequencing kits.
  • Long insert recipe: If you are using Cloudbreak or Cloudbreak Freestyle chemistry and libraries with > 1000 bp DNA inserts, use the long insert recipe. The recipe is only applicable for 2 x 75 and 2 x 150 sequencing kits, as 2 x 300 sequencing kits already account for long insert conditions.
  • AVITI OS 3.0.0 recipe: For use with AVITI OS 3.0.0 Cloudbreak planned runs.
• Uploaded recipe: Element prepares an encrypted, custom recipe package as a .rec file for upload to a planned run. To obtain a custom recipe for a specific use case, contact Element Technical Support.

PMG Shift

The PMG Shift feature allows a user to shift (dark-cycle) up to 20 cycles of PMG (Polony Map Generation). To use PMG shift:

• Enter the number of cycles (0-20) to shift Polony Map Generation.
• This value will count towards the total number of cycles. An error is returned if the kit maximum is exceeded.
• If you do not use the PMG Shift feature, the default value is 0 cycles.
• Available for Cloudbreak and Cloudbreak Freestyle Adept and Third Party libraries.

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 and settings specified inside the manifest will not result in demultiplexing errors. 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 cytoprofiling run manifest, see the Run Manifest Documentation.

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. Select the Run Name, or 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.