ONT read integration about hifiasm HOT 8 CLOSED

In my experience, the --ul option significantly increases the run time. For example, I ran a job on a relatively small genome (450 MB) with the --ul option, and it took about 27 hours to finish. Without the --ul option, the same job took only 5 hours.

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Ah thanks. I will let it spool and update once the job ends.

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Hello. Just updating that the run completed without issue. It took ~150 compute days. Genome was ~ 700 Mb.

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Hello. Just updating that the run completed without issue. It took ~150 compute days. Genome was ~ 700 Mb.

Thanks a lot. But 150 compute days might be too slow. How much coverage do you have?

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Using averaged read length:
Estimated coverage for PacBio = ~28x
Estimated coverage for ONT = >100x (but using median length is ~70x)

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So the total CPU hours are 3600?

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Yes. I am also assuming that I did something wrong, but so far the outputs look like what I'd expect based on QC and compared to other assemblies.

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Thanks a lot. Probably because the UL step is too slow due to the very high coverage.

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