Is minimum abundance filter used in Cuttlefish2/Minia?

IndexThePlanet / Logan

Logan Unitigs and Contigs

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Is minimum abundance filter used in Cuttlefish2/Minia? #9

Closed mr-eyes closed 2 months ago

mr-eyes commented 2 months ago

Hey Rayan,

I was exploring some compressed logan runs and noticed a significant loss of k-mers when comparing unitigs/contigs to the full read content in the SRA. Are you applying a filter to exclude k-mers with low abundance (e.g., 1 or 2), as they're likely errors? Or maybe I am getting something wrong about how Logan works.

Thanks!

mr-eyes commented 2 months ago

I think it was a dumb question, it totally make sense to trim errors. I will appreciate if you can post the abundance cutoff used. Thanks!

rchikhi commented 2 months ago

hi, yes, k-mers seen only once are discarded

mr-eyes commented 2 months ago

thx!