search

maickrau / GraphAligner

MIT License
261 stars 32 forks source link

Optimal alignment #80

Closed abanerjee10 closed 1 year ago

abanerjee10 commented 1 year ago

What is the recommended method for doing optimal alignment with GraphAligner?

Does the hidden argument --seedless-DP accomplish this, and is there a faster option available?

maickrau commented 1 year ago

There's no option for doing guaranteed optimal alignment. You can try something like --seedless-DP -b 100000 --precise-clipping 0.502 --X-drop 1000000 which should have a high probability of returning optimal alignments but not guaranteed.

abanerjee10 commented 1 year ago

I see, I believed that guaranteeing optimal alignment was possible. Thank you for your help!