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muellan / metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
GNU General Public License v3.0
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Strain Level Database #13

Closed punnettsun closed 3 years ago

punnettsun commented 3 years ago

Hello,

I noticed that MetaCache can classify reads at the sequence level. If I had my own strain level database, would I be able to use MetaCache to classify reads at strain level?

Thank you.

muellan commented 3 years ago

Hi,

yes, it's possible to classify at any level, if the reference sequences/genomes are annotated accordingly.

We didn't do many systematic tests below species level. So I can't point you to any publication regarding what levels of sensitivity or precision to expect with the default settings. That said, I would first try it using the default settings. If too many reads are unmapped, you could increase the sketch size (command line parameter '-sketchlen') when building the database. This should increase sensitivity and precision at the expense of higher memory consumption.

punnettsun commented 3 years ago

Great, thank you for the clarification and for the quick response!