search

DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
706 stars 270 forks source link

Species-level 16S kraken2 database? #862

Open DntBScrdDv opened 1 month ago

DntBScrdDv commented 1 month ago

Hi all,

I'm in need of a species-level 16S database. I had relied on the rdp database on other analysis platforms (e.g. FROGS) but the pre-built kraken2 rdp database only goes to genus-level.

I built a database from the RefSeq database but it is missing many key taxa (e.g. candidatus Omnitrophus).

Does anyone know of a species-level 16S database for kraken2 that is broader than RefSeg? e.g. a species-level Silva or RDP?

Many thanks

ChillarAnand commented 1 month ago

Kraken 2 / Bracken 16s RNA indexes are available for Greenegenes, RDP, Silva.

https://benlangmead.github.io/aws-indexes/k2

Does this help?

DntBScrdDv commented 1 month ago

Hi @ChillarAnand ,

Many thanks for your reply. Unfortunately, no - this doesn't help. The Kraken2 RDP and Silva databases are limited to genus level, while GreenGenes has not been updated since - I think - 2016.