Kraken2 with phylogeny as input (instead of taxonomy)?
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5 months ago
cjb ▴ 10

The way kraken2 assigns a kmer to a genus when the kmer is found in multiple species seems to be a generalizable method that could be extended to a phylogeny. Instead of relying on taxonomic relationships, a kmer could be assigned to the last common ancestor of the species sharing it.

If kraken2 does not actually require taxonomic division names in the taxonomy, would it be possible to edit the taxonomy files to use arbitrary names for nodes? If bracken could read the output then abundances of clades in the phylogeny could be computed.

Specifically:

Has anyone represented a phylogeny by editing a taxonomy to have arbitrary division names, and gotten kraken2 to work?

And even better gotten bracken to compute on the output?

kraken phylogeny • 210 views
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