Databases for RefineM
---------------------

Provided files span the set of representative genomes at GTDB.


Example usage:
--------------
Decompress the protein and 16S rRNA databases:
> tar -xzf gtdb_r80_protein_db.2017-11-09.tar.gz
> tar -xzf gtdb_r80_ssu_db.2018-01-18.tar.gz

DIAMOND and BLAST protein databases can then be created as follows:
> diamond makedb -p 32 -d gtdb_r80_protein_db.2017-11-09.faa --in gtdb_r80_protein_db.2017-11-09.faa
> makeblastdb -dbtype prot -in gtdb_r80_protein_db.2017-11-09.faa

A BLAST database for the 16S rRNA genes can be created with:
> makeblastdb -dbtype nucl -in gtdb_r80_ssu_db.2018-01-18.fna


[GTDB r95]
gtdb_r95_protein_db.2020-07-30.faa.gz   GTDB r95 (http://gtdb.ecogenomic.org/). The provided FASTA file must be 
                                        formatted to a DIAMOND or BLAST database before use.
                                        
gtdb_r95_taxonomy.2020-07-30.tsv:       Taxonomy file contains GTDB taxonomy information for the 31,910 genomes.

- the 16S file for GTDB R80 is recommended for use with RefineM


[GTDB r89]
gtdb_r89_protein_db.2019-09-27.faa.gz   GTDB r89 (http://gtdb.ecogenomic.org/). The provided FASTA file must be 
                                        formatted to a DIAMOND or BLAST database before use.
                                        
gtdb_r89_taxonomy.2019-09-27.tsv:       Taxonomy file contains GTDB taxonomy information for the 24,706 genomes.

- the 16S file for GTDB R80 is recommended for use with RefineM


[GTDB r86]
gtdb_r86_protein_db.2017-11-09.tar.gz:  Consists of 92,117,422 proteins from the 27,372 genomes used to defined 
                                        GTDB r86 (http://gtdb.ecogenomic.org/). The provided FASTA file must be 
                                        formatted to a DIAMOND or BLAST database before use.
                                        
gtdb_r80_taxonomy.2017-12-15.tsv:       Taxonomy file contains GTDB taxonomy information for the 27,372 genomes.

- the 16S file for GTDB R80 is recommended for use with RefineM


[GTDB r80]

gtdb_r80_protein_db.2017-11-09.tar.gz:  Consists of 73,689,358 proteins from the 23,170 genomes used to defined 
                                        GTDB r80 (http://gtdb.ecogenomic.org/). The provided FASTA file must be 
                                        formatted to a DIAMOND or BLAST database before use.

gtdb_r80_ssu_db.2018-01-18.tar.gz:      16S rRNA genes >1200 bp identified within the 23,170 genomes used to define 
                                        GTDB r80 (http://gtdb.ecogenomic.org/). The provided FASTA file must be formatted
                                        to a BLAST database before use. 

gtdb_r80_taxonomy.2017-12-15.tsv:       Taxonomy file contains GTDB taxonomy information for the 23,170 genomes.