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marbl / Winnowmap

Long read / genome alignment software
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Mapping setting advice #13

Closed GuillaumeHolley closed 3 years ago

GuillaumeHolley commented 3 years ago

Hi,

I am trying to use Winnowmap to map long reads with an error rate around 1.5-3%. I tried both the map-ont and map-pb presets and the difference between the two can be quite big. Any recommendation on a preset or some specific settings?

Thank you. Guillaume

cjain7 commented 3 years ago

What are the read lengths like?

GuillaumeHolley commented 3 years ago

Roughly 20 to 25 kb.

cjain7 commented 3 years ago

You can go with map-pb in this case.

GuillaumeHolley commented 3 years ago

I appreciate the feedback, thank you!