Main Database Files

File	Description
KSGP_v1.0.fasta	Version 1 of KSGP database. Contains cleaned GTDB SSU sequences; and Eukaryote sequences from PR2 with their original annotations combined with reannotated SSU rRNA sequences from both Karst et al and Archaea 16S sequences from SILVA. Please note that the taxonomic hierarchy used by PR2 is not compatible with that used by SILVA or NCBI.
KSGP_v1.0.tax	LotuS2 tax file for version 1.0 of KSGP database
KSGP_v1.0.tar.gz	Complete KSGP v1.0 database
KSGP_v3.1.fasta	Version 3.1 of KSGP database. Contains cleaned GTDB SSU sequences; and Eukaryote sequences from PR2 with their original annotations combined with reannotated SSU rRNA sequences from both Karst et al and Archaea 16S sequences from SILVA. Please note that the taxonomic hierarchy used by PR2 is not compatible with that used by SILVA or NCBI.
KSGP_v3.1.tax	LotuS2 tax file for version 3.1 of KSGP database
KSGP_v3.1.tar.gz	Complete KSGP v3.1 database
KSGP_v4.0.fasta	Version 4.0 of KSGP database. The KSGP and GTDB+ sequence files have now had sequences that are contaminated with LSU sequence removed. KSGP_v4.0.tax is generated using SINTAX; KSGP_v4.0_lca.tax using USEARCH matches from GTDB+ and LCA from LotuS2; KSGP_v4.0_plus.tax is based on KSGP_v4.0_lca.tax with taxonomic uncertainties not resolved by LCA replaced with cluster centroids of arbitrary taxa at approximately that taxonomic rank. In Eukaryome, sequences do not all have taxonomic assignments at levels down to species, which means that the same is true for these sequences in GTDB+. KSGP_v4.0_plus2.tax is an attempt to remedy this by applying the same process used to annotate unknown sequences in KSGP_v4.0_plus and where necessary completing the taxonomic assignments at lower levels using arbitrary taxa characterised by a sequence that makes up the cluster centroid. We recommend using KSGP_v4.0_plus2.tax. See the readme archived within the tar.gz file for full details.
KSGP_v4.0_plus2.tax	LotuS3 tax file for version 4.0 of KSGP database
KSGP_v4.0.tar.gz	Complete KSGP v4.0 database

Auxilliary Files

File	Description
GTDB_plus_v1.0.fasta	Version 1 of GTDB+ database (cleaned GTDB plus eukaryotes from PR2). Please note that the taxonomic hierarchy used by PR2 is not compatible with that used by SILVA or NCBI.
GTDB_plus_v1.0.tax	LotuS2 tax file for version 1.0 of GTDB+ database
GTDB_cleaned_v1.0.fasta	Cleaned and deduplicated GTDB Fasta File with domain level misassignments removed – should be combined with a database of eukaryote 18S sequences, such as PR2
GTB_cleaned_v1.0.tax	Corresponding LotuS2 Tax file
GTDB_214_SSU_sequences_removed_as_wrong_domain.csv	SSU sequences in GTDB assigned to a different domain by RDP Classify and removed. The file includes both the original GTDB classification and RDP Classify annotation.

Data sources

GTDB+ contains sequences and taxonomic assignments from Version 214.0 of GTDB and version 5.0 or PR2. KSPG also contains sequences from SILVA SSURef NR99, version 138.1 and ENA accession GCA_900214305.