Introduction
Expert Mode HD adjusts polony mapping to enable an increase in sequencing run pre-filter output by 20-70% with a minor quality impact of 1-3% Q30. 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.
Applications
Expert Mode HD can help with applications that might need a boost in throughput but can tolerate minor impacts to quality and secondary metrics. Mapping or counting applications are a good fit, 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 RNA-Seq, scRNA-Seq, WES, and WGS sequencing runs, is available in the Expert Mode HD Technical Note (LT-00039).
Implementation
Expert Mode HD can be accessed in the Advanced Run Settings menu of the AVITI, under the label Polony Density, which includes two options, Standard (default) and High Density. To use Expert Mode HD, select the High Density setting. For more information on how to configure Advanced Run Settings, visit the Run Setup section of the CloudbreakTM Sequencing User Guide (MA-00058). Sequencing runs that used Expert Mode HD for polony mapping cannot be reprocessed using the standard polony mapping algorithm. Expert Mode HD can be paired with flexible filtering settings in Bases2Fastq, allowing users to tune the number and quality of reads that are output during fastq file generation. The quality filtering settings in Bases2Fastq are adjusted using the --filter-mask optional argument, which is separate from Expert Mode HD.