search

biocore / greengenes2

Processing support for Greengenes2
11 stars 2 forks source link

Using GreenGenes2 as Kraken 2 DB. #6

Closed VoronDM closed 10 months ago

VoronDM commented 10 months ago

Until the major update of GreenGenes to GreenGenes2, it can be easily used as a custom 16S database for Kraken 2. To create such database, only two files was needed - ${GG_VERSION}.fasta.gz and ${GG_VERSION}_taxonomy.txt.gz. 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 possible to implement a database compatible with the previous format?

wasade commented 10 months ago

Hi @VoronDM, it sounds like the kraken2 support script itself needs to be updated. I recommend opening an issue with that project. I'm not familiar with the script, but I would imagine it would need to use the backbone fasta and tax files available in the release

wasade commented 10 months ago

...@VoronDM, if you open an issue with that project, could you please tag me so I can coordinate with them?