search

DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
687 stars 266 forks source link

Using GreenGenes2 as Kraken2 custom DB #774

Open VoronDM opened 7 months ago

VoronDM commented 7 months ago

Until the major update of GreenGenes DB to GreenGenes2, it can be easily used as a custom 16S database for Kraken 2. This will be implemented as a simple bash script (https://github.com/DerrickWood/kraken2/blob/master/scripts/16S_gg_installation.sh). Since after a major update the structure of the GG2 database has changed, it is now not clear how it can be used with the Kraken2. Is it plan to make db build script update for using GG2 as Kraken2 custom DB?

AlexandreThibodeauUdM commented 7 months ago

I think Greengene2 wil be usefull only for specific tools as it is now in a tree form from what I can understand from it. Do not think it will be usable for Kraken2.