Observation: Reads get split at certain intervals more often. about herro HOT 3 OPEN

Hi @bpanda-dev

This is likely explained in the following excerpt from the consensus subsection inside methods section in the preprint (which was posted one day after your question).

If a window contains fewer than two alignments, the window is discarded, and the read is split.

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That is an interesting observation. I will just point out that herro window size (for the inference) is 4096 by default. I wonder if the regular spikes you see are multiples of that number. If they are, then that would be the avenue to explore.

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@sivico26,
Yes, it seems to be an artefact of the model window size since these spikes are in and around the multiples of 4096 (Please refer to the figure attached, uses a different dataset from the plot in my above comment).

I had some more questions:

1. How does this splitting pattern affect the output assembly now that we have shorter reads?
2. Why are only some raw reads split this way and not all? Does this happen when the read error rate is high at the edges of windows(4096 length)?

Thank You.

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