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Aligning to distant homologues #50

Open

ens-sb opened this issue Oct 24, 2023 · 2 comments

ens-sb commented Oct 24, 2023

What would be a recommended setting for a slower but more sensitive alignment to distant homologues?

Owner

lh3 commented Oct 24, 2023 •

edited

You may consider:

-M0 (denser seeds)
-M0 -k5 (smaller k-mer)

Note that these may only improve sensitivity a little. I need to redesign the seeding algorithm for higher sensitivity.

Author

ens-sb commented Oct 24, 2023

Thanks a lot!

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