AVITI OS v2.0.0 Release Notes

The AVITI OS v_2.0.0 Software is now available. This version is required for all instruments, and upgrades will be performed in coordination with local support teams. Details of this release are described below.

Workflow and UX

  • The software introduces an improved user workflow, experience, and design.
  • The user must accept the End User Licensing Agreement (EULA) prior to use.
  • Buffer and sequencing cartridge loading takes place before inputing run information.
  • The software includes improved handling for critical errors, such as waste module leaks.
  • LED status notifications have been added for the following situations:
    • LED bars display white while the instrument is initializing.
    • For each side, the LED bar is blue during the wash workflow and pulses blue while the instrument executes wash recipes.
    • For each side, the LED bar pulses red when a run fails until the failure notification is marked as ‘read’. The issue the instrument was experiencing (e.g leak detected) must be resolved on that side to start a subsequent run.
    • For each side, the LED bars pulse orange when a warning occurs until the warning notification is marked as ‘read’.

Run Manifest

  • Run manifests no longer contain the [RunParameters] section. Users input run parameters directly into AvitiOS during the Run setup, and AvitiOS records in the output RunParameters.json file as an execution record. There are no changes to the workflow users follow on the instrument for the run manifest.
    • Note: If RunParameters are included in a manifest, the AvitiOS system ignores the parameters, and the run setup form no longer pre-populates with RunParameter values.

New Features

  • Onboard Indexing Assignment Rates
    • Indexing assignment runs automatically on the instrument after the index cycles specified in the Index1Mask and Index2Mask of the manifest complete.
      • If masks are not provided, the masks default to the full indexing reads.
      • Onboard indexing assignment only applies to runs with fewer than 384 samples.
    • The instrument displays %Assigned, %Perfect Match, and the number of samples with low representation (<10k reads).
  • End-user initiated software and firmware updates are now available. After installing AVITI OS v2.0.0, users can manage software and firmware updates for both online and offline instruments without requiring Element Service & Support on site.
  • Storage connections
    • Enable user specified default storage connection for the instrument if an instrument has more than one storage connection.
    • Add support for Kerberos in addition to NTLMv2 for SMB authentication.
    • Allow users to configure a hard drive or USB as a storage connection for sequencing run data.
    • If the instrument runs out of disk space (e.g. due to a network connection issue), the instrument automatically pauses the run. The run automatically resumes after space becomes available.
    • For offline instruments, the software lets users configure regular automated export of logs and offline telemetry data to the storage connection of their choice. After the data is off the instrument, users can work with Element to regularly upload the data into Element’s systems for improved troubleshooting and support. Contact Technical Support to learn more.
  • Output Data
    • The software now outputs a statistics file to the run folder at the end of the run. This statistics file contains the run name, run ID, number of raw polonies, number of polonies passing filter, % polonies passing filter, total yield, indexing assignment metrics, % Q30 per cycle, and % PhiX error per cycle.
    • The software obfuscates Sample Names and the Run Description in all logs and telemetry data.
    • Basecall files are now archived per cycle into a zip archive, reducing the total number of files output. This change requires an upgrade to Bases2Fastq v1.4.0 to support the new file format.
  • Online local authentication mode is now available for sites that prefer local authentication for online instruments (due to allowlisting or other issues). Contact Technical Support to enable this mode on your instrument.
  • The indexing assignment rate is improved in situations where the set of indices is small or poorly balanced.
  • There is improved basecalling for low diversity runs. We require high diversity within the first 4 cycles of read 1 but not for other cycles.

Resolved Issues

  • Run Name Errors
    • In the Aviti 1.x series, if the same run name was used within 7 days without a powercycle in-between, the software rejected some internal analysis jobs, leading to the second named run failing.
    • In the Aviti 1.x series, if the run name included the NT_ and transferred to local storage over SMB, the software incorrectly interpreted an error and the run failed to transfer.
  • In the Aviti 1.x series, users encountered a “404” page not found error if they attempted to Manage Connections from the Home screen on an instrument with no configured storage connections.
  • In the Aviti 1.x series, if an instrument was in a timezone with a positive increment to UTC time (for example, time zones in Europe or Asia), the priming timer countdown started and stayed at 00:00 while priming executed.