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smangul1 / MiCoP

MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
GNU General Public License v3.0
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Pre-filtering? #1

Closed dkoslicki closed 6 years ago

dkoslicki commented 6 years ago

Did you want to implement the CMash pre-filtering to enable profiling of bacteria as well?

nlapier2 commented 6 years ago

I am interested in including CMash, but we'd have to figure out some clever way of avoiding the re-indexing of the reduced databases after applying CMash. Normally indexing a database with something like BWA would only have to be done once, but every time we reduce the database based on some reads using CMash, we'd have to re-index it before performing alignment.