Does the AVITI™ bin quality scores?

Question:

Does the AVITI bin quality scores?

Answer:

No, the AVITI reports continuous quality scores.

Summary

The AVITI reports continuous quality scores (Q-scores).

• Continuous Q-scores provide more granularity in quality data
• Binned Q-scores save computational space, but can lose granularity in quality data
• Analyses performed by legacy software programmed to handle only binned data can be affected when continuous data is used as input

Considerations

Binned Data

“Binned data” refers to quality scores that are grouped into "bins", or levels wherein a range of probabilities are collapsed into a single representative value. While this approach saves computational space, it results in a loss of granularity in the quality data.

Continuous Data (AVITI)

The AVITI system reports the full range of integer quality scores based on the actual probability of a base call error. Representing Q-scores continuously provides a more precise representation of data quality across the length of the read for more nuanced variant calling.

Software Compatibility

Some legacy software is programmed to expect only binned Q-scores as input. As a result, these legacy software can experience "read loss" if they are programmed to handle binned data and cannot correctly interpret the continuous scores from an AVITI sequencing run. If you experience unexpected read loss during secondary analysis of your data, check if your software expects binned (not continuous) Q-scores.