Does the provided NT index have low complexity?

DaehwanKimLab / centrifuge

Classifier for metagenomic sequences

GNU General Public License v3.0

237 stars 73 forks source link

Does the provided NT index have low complexity? #132

Open wpearman1996 opened 6 years ago

wpearman1996 commented 6 years ago

Does the NT index available to download have low complexity regions filtered out? and is this the only method for dealing with low complexity in Centrifuge? I've tried to read around to see how centrifuge manages low complexity regions, but i'm not sure yet. Does Centrifuge only manage low complexity when the index is created? or when the algorithm is being run? or both? Cheers,

khyox commented 6 years ago

I think the comments in issue https://github.com/infphilo/centrifuge/issues/99 (Questions about NT index generation) can help you.