Remote Run Monitoring

Elembio Cloud synchronizes with connected systems to update run monitoring information in real time on the following pages:

• Active Runs: Summarizes information for the most recent runs, grouped by instrument.
• All Runs: Displays information for active and historical runs from connected systems.
• Run Details: Displays detailed information for a run.

Active Runs

Cards on the Active Runs page display high-level information about sequencing runs. The page orders the cards by instrument and side A or B, mimicking the instrument display. A dynamic gauge graphic on each card visualizes the run stage and the number of cycles completed.

The cards update as follows.

• When a run is in progress on one side, the card information updates in real time. The card links to the Run Details page.
• When a run is no longer in progress, the card displays information for the last run executed. The card links to the Run Details page for that run, and the card footer updates to indicate that the side is available.
• The most recent run status always appears as a badge in the top-right corner of the card.

Figure 1: Example cards on Active Runs page

Gauge Graphic

The gauge graphic displays each stage of a run, from initiation to completion. The gauge changes colors to indicate different statuses. The center of the gauge displays the time elapsed. Under the time, the gauge displays the current step for the run.

Run Statuses

Status	Gauge Color	Description
Priming/Primed	Blue	The run is in setup mode. Metrics do not populate before sequencing starts.
Sequencing	Blue	The run is actively progressing. Metrics populate as they become available.
Pausing/Paused	Orange	If you request a flexible start, the run pauses. Resumption of the run is automatic.
Completed	Green	The run successfully finishes. The instrument transfers all data to the selected storage location.
Failed	Red	During the run, the instrument encounters a critical issue and does not successfully finish. Data analysis completes up to and including the last successfully sequenced cycle. The instrument transfers available data to the selected storage location.
Stopped	Teal	A user stops the run before it finishes. Data analysis completes up to and including the last successfully sequenced cycle. The instrument transfers all data to the selected storage location.

All Runs

The All Runs table displays a full list of data for active and historical runs. The table includes buttons to filter runs, hide and show columns, and navigate table pages. The Run Name and Run ID fields link to the Run Details page for a run.

Remove a Run

The All Runs page also lets you remove a run. Removed runs no longer display in Elembio Cloud. However, the data from removed runs remains archived and hidden. If you accidentally remove a run, contact Element Technical Support to restore it.

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

Run Details

A complete record of a sequencing run is available on the Run Details page. The following features appear on the page:

• Run Overview: Visualizes the current run status in a gauge graphic.
• Primary Analysis Metrics: Displays key run metrics, including reads, yield, Q30, and percent reads passing filter (% PF).
• Run Setup: Displays run setup details, including the library type, library structure, sequencing kit, and the number of library pools.
• Run Configuration: Displays detailed information about the run, cartridge, buffer bottle, and flow cell.
• Primary Analysis: Graphs metrics, such as PhiX error rates and Q30, throughout Read 1 (R1) and Read 2 (R2).

Primary Analysis Charts

On the Primary Analysis tab, charts graph the following quality metrics throughout the sequencing run. Available metrics depend on the AVITI Operating Software (AVITI OS) version. If using the individually addressable lanes add-on, buttons above the charts allow you to select Library Pool 1 or Library Pool 2.

Each chart includes buttons to expand the graph and export it as an image.

Chart	AVITI OS Version	Description
Q-Scores	AVITI OS v1.0.0+ for Q30 AVITI OS v2.2.0+ for Q40 and average Q-score	The percentage of base calls in each Read 1 and Read 2 cycle with a Q-score ≥ Q30 and a Q-score ≥ Q40. The chart also displays the average Q-score for each cycle. Q30 indicates an incorrect base call probability of 1 in 1000, which equals a 99.9% confidence rate. Q40 indicates an incorrect base call probability of 1 in 10,000, which equals a 99.99% confidence rate. Average Q-score is the median Q-score.
PhiX Error Rate	AVITI OS v1.0.0+ for PhiX error rate AVITI OS v2.2.0+ for % PhiX Aligned	The percentage of control reads in each Read 1 and Read 2 cycle that do not align to a spike-in of PhiX Control Library. The % PhiX Aligned metric for R1 and R2 appears at the top of the chart.
Indexing Assignment	AVITI OS v2.0.0+	The percentages of reads assigned with a perfect index match or an index mismatch. Expansion of the chart displays tables that list the top samples with a mismatch and with low representation.
Base Composition	AVITI OS v2.2.0+	The percentage of adenine (A), cytosine (C), guanine (G), and thymine (T) in each cycle for Read 1, Read 2, Index 1, and Index 2.
Image Thumbnail	AVITI OS v2.2.0+	The image thumbnail displays a snapshot of the polonies on a tile from the first cycle of the run. The image indicates sample density and loading concentration on the flow cell. Use the image as a quality check to identify overloaded or underloaded flow cells.

Troubleshooting Run Monitoring

If data in Elembio Cloud do not seem to be in sync with data on the instrument, the instrument might have lost a network connection. Reconnect the instrument to the network, and then make sure the data update in Elembio Cloud. If the issue persists, contact Element Technical Support.