When should I enable Expert Mode HD for my sequencing run? | Element Biosciences

Question

When should I enable Expert Mode HD for my sequencing run on AVITI?

Answer

For assays that have otherwise reasonable performance on the AVITI, Expert Mode HD can provide an increase in output with equivalent or slightly reduced performance in secondary analysis.

Summary

• Expert Mode HD adjusts polony mapping on the AVITI system to enable an increase in sequencing pre-filter output by 20–70% with a minor quality impact of 1–3% Q30
• Expert Mode HD can help with applications that might need a boost in throughput but can tolerate minor impacts to quality and secondary metrics
• While the AVITI24™ system removes Expert Mode HD with most applications while maintaining AVITI quality, Expert Mode HD can be used for 2x300 sequencing runs on AVITI24

Considerations

Applications

Mapping or counting applications are a good fit for Expert Mode HD on AVITI, as are those applications that need to consistently meet high coverage targets with limited requeues of samples. More detailed information about Expert Mode HD, including comparison experiments with various applications, is available in the Expert Mode HD Technical Note.

Implementation

Expert Mode HD can be accessed in the Advanced Run Settings menu of the AVITI, under the label Polony Density. This label includes two options, Standard (default) and High Density.

To use Expert Mode HD, select the High Density setting. For more help configuring Advanced Run Settings, visit the Run Setup section of the Cloudbreak^TM Sequencing User Guide.

The AVITI24 system removes Expert Mode HD with most applications while maintaining AVITI quality, but Expert Mode HD can be used for 2x300 sequencing runs on AVITI24.

Sequencing runs that used Expert Mode HD for polony mapping cannot be reprocessed using the standard polony mapping algorithm. You can pair Expert Mode HD with flexible filtering settings in Bases2Fastq to tune the number and quality of reads that are output during fastq file generation. You can also adjust quality filtering settings in Bases2Fastq using the --filter-mask optional argument, which is separate from Expert Mode HD.