Use GTDB genomes (representatives or all) instead of NCBI

FOI-Bioinformatics / flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

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Use GTDB genomes (representatives or all) instead of NCBI #28

Closed davve2 closed 3 years ago

davve2 commented 3 years ago

GTDB supplies several genome sets for their databases on their download page,

Implement a function that alternatively can use these genome sets instead of downloading genomes from NCBI.

https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/genomic_files_reps/ https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/genomic_files_all/