Questions regarding differences between Dorado correct and Herro

[hanqu24]

Hello,

Thank you for developing such a user-friendly and efficient tool! I recently tried running both Dorado correct and Herro, and I have a few questions:

1. Herro includes additional preprocessing steps such as adaptor removal, read splitting on adaptors, and filtering out short and low-quality reads. In contrast, Dorado doesn’t seem to include these steps, though I understand the usage of window size settings in Dorado. Does this mean that using Dorado trim + Dorado correct is sufficient, or would preprocessing with Herro before running Dorado correct yield better results?

2. Herro uses different parameters in minimap2 for UL and non-UL data. Are similar parameter distinctions used in Dorado correct? Also, do these settings work effectively for other organisms, such as plants?

3. I’m working with a very large ONT dataset (>100X coverage), which would take a considerable amount of time to process in full. Would the additional time spent on processing the entire dataset significantly improve the results? If I downsample to a certain coverage (e.g., 60X), would the results remain comparable? Additionally, would random downsampling or length-based downsampling yield better outcomes?

I appreciate your time and guidance on these questions. Thank you again for your incredible work!
Han