How does Centrifuge classify reads at subspecies/strain level given NCBI taxonomy?

DaehwanKimLab / centrifuge

Classifier for metagenomic sequences

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How does Centrifuge classify reads at subspecies/strain level given NCBI taxonomy? #200

Open punnettsun opened 4 years ago

punnettsun commented 4 years ago

Hello,

I took a look at the NCBI taxonomy files (names.dmp, nodes.dmp). In the nodes.dmp file, all I see are the ranks from species to superkingdom level, so how does Centrifuge classify reads at subspecies/strain level? Where does it get the strain information from?

Thank you.

MardahlM commented 2 years ago

I am also interested in the answer to this question. Cheers, Maibritt