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query/parsing/merging tool for NCBI/GTDB/SILVA taxonomies
produces two files:
- df_gtdb_to_ncbi_to_gg_silva_archaea_plus_bacteria_trim.tsv
GTDB_accession RefSeq_or_GenBank ncbi_genbank_assembly_accession ncbi_taxid gtdb_taxonomy ncbi_taxonomy ncbi_taxonomy_unfiltered ssu_gg_taxonomy ssu_silva_taxonomy
GB_GCA_000007185.1 GB GCA_000007185.1 190192 d__Archaea;p__Methanobacteriota;c__Methanopyri;o__Methanopyrales;f__Methanopyraceae;g__Methanopyrus;s__Methanopyrus kandleri d__Archaea;p__Euryarchaeota;c__Methanopyri;o__Methanopyrales;f__Methanopyraceae;g__Methanopyrus;s__Methanopyrus kandleri d__Archaea;p__Euryarchaeota;c__Methanopyri;o__Methanopyrales;f__Methanopyraceae;g__Methanopyrus;s__Methanopyrus kandleri;x__Methanopyrus kandleri AV19k__Archaea;p__Euryarchaeota;c__Methanopyri;o__Methanopyrales;f__Methanopyraceae;g__Methanopyrus;s__kandleri Archaea;Euryarchaeota;Methanopyri;Methanopyrales;Methanopyraceae;Methanopyrus;Methanopyrus kandleri AV19
GB_GCA_000007345.1 GB GCA_000007345.1 188937 d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina;s__Methanosarcina acetivorans d__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina;s__Methanosarcina acetivorans d__Archaea;p__Euryarchaeota;x__Stenosarchaea group;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina;s__Methanosarcina acetivorans;x__Methanosarcina acetivorans C2A none Archaea;Euryarchaeota;Methanomicrobia;Methanosarcinales;Methanosarcinaceae;Methanosarcina;Methanosarcina acetivorans C2A
GB_GCA_000008085.1 GB GCA_000008085.1 228908 d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Nanoarchaeales;f__Nanoarchaeaceae;g__Nanoarchaeum;s__Nanoarchaeum equitans d__Archaea;p__Nanoarchaeota;c__;o__Nanoarchaeales;f__Nanoarchaeaceae;g__Nanoarchaeum;s__Nanoarchaeum equitans d__Archaea;x__DPANN group;p__Nanoarchaeota;o__Nanoarchaeales;f__Nanoarchaeaceae;g__Nanoarchaeum;s__Nanoarchaeum equitans;x__Nanoarchaeum equitans Kin4-M k__Archaea;p__Nanoarchaeota;c__[Nanoarchaeoti];o__[Nanoarchaeotales];f__[Nanoarchaeotaceae];g__Nanoarchaeum;s__equitans Kin4-MArchaea;Nanoarchaeaeota;Nanoarchaeia;Nanoarchaeales;Nanoarchaeaceae;Nanoarchaeum;Nanoarchaeum equitans
GB_GCA_000011125.1 GB GCA_000011125.1 272557 d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Desulfurococcales;f__Acidilobaceae;g__Aeropyrum;s__Aeropyrum pernix d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Desulfurococcales;f__Desulfurococcaceae;g__Aeropyrum;s__Aeropyrum pernix d__Archaea;x__TACK group;p__Crenarchaeota;c__Thermoprotei;o__Desulfurococcales;f__Desulfurococcaceae;g__Aeropyrum;s__Aeropyrum pernix;x__Aeropyrum pernix K1 k__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Desulfurococcales;f__Desulfurococcaceae;g__Aeropyrum;s__ Archaea;Crenarchaeota;Thermoprotei;Desulfurococcales;Acidilobaceae;Aeropyrum;Aeropyrum camini SY1 = JCM 12091
GB_GCA_000014945.1 GB GCA_000014945.1 349307 d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix_B;s__Methanothrix_B thermoacetophila d__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanotrichaceae;g__Methanothrix;s__Methanothrix thermoacetophila d__Archaea;p__Euryarchaeota;x__Stenosarchaea group;c__Methanomicrobia;o__Methanosarcinales;f__Methanotrichaceae;g__Methanothrix;s__Methanothrix thermoacetophila;x__Methanothrix thermoacetophila PT k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta;s__ Archaea;Euryarchaeota;Methanomicrobia;Methanosarcinales;Methanosaetaceae;Methanosaeta;Methanosaeta thermophila PT
GB_GCA_000015805.1 GB GCA_000015805.1 410359 d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__Pyrobaculum calidifontis d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__Pyrobaculum calidifontis d__Archaea;x__TACK group;p__Crenarchaeota;c__Thermoprotei;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__Pyrobaculum calidifontis;x__Pyrobaculum calidifontis JCM 11548 k__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__ Archaea;Crenarchaeota;Thermoprotei;Thermoproteales;Thermoproteaceae;Pyrobaculum;Pyrobaculum calidifontis
GB_GCA_000018465.1 GB GCA_000018465.1 436308 d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus;s__Nitrosopumilus maritimus d__Archaea;p__Thaumarchaeota;c__;o__Nitrosopumilales;f__Nitrosopumilaceae;g__Nitrosopumilus;s__Nitrosopumilus maritimus d__Archaea;x__TACK group;p__Thaumarchaeota;o__Nitrosopumilales;f__Nitrosopumilaceae;g__Nitrosopumilus;s__Nitrosopumilus maritimus;x__Nitrosopumilus maritimus SCM1 k__Archaea;p__Crenarchaeota;c__Thaumarchaeota;o__Cenarchaeales;f__Cenarchaeaceae;g__Nitrosopumilus;s__ Archaea;Thaumarchaeota;Nitrososphaeria;Nitrosopumilales;Nitrosopumilaceae;Candidatus Nitrosopumilus;Nitrosopumilus maritimus SCM1
GB_GCA_000019805.1 GB GCA_000019805.1 444157 d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__Pyrobaculum neutrophilum d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__Pyrobaculum neutrophilum d__Archaea;x__TACK group;p__Crenarchaeota;c__Thermoprotei;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__Pyrobaculum neutrophilum;x__Pyrobaculum neutrophilum V24Sta k__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Thermoproteales;f__Thermoproteaceae;g__Pyrobaculum;s__ Archaea;Crenarchaeota;Thermoprotei;Thermoproteales;Thermoproteaceae;Pyrobaculum;Pyrobaculum neutrophilum V24Sta
GB_GCA_000022445.1 GB GCA_000022445.1 426118 d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus;s__Saccharolobus islandicus d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Sulfolobales;f__Sulfolobaceae;g__Sulfolobus;s__Sulfolobus islandicus d__Archaea;x__TACK group;p__Crenarchaeota;c__Thermoprotei;o__Sulfolobales;f__Sulfolobaceae;g__Sulfolobus;s__Sulfolobus islandicus;x__Sulfolobus islandicus M.16.4 k__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Sulfolobales;f__Sulfolobaceae;g__Sulfolobus;s__islandicus Archaea;Crenarchaeota;Thermoprotei;Sulfolobales;Sulfolobaceae;Sulfolobus;Sulfolobus islandicus M.16.4
- df_silva_to_ncbi.tsv
SLV_accession NCBI_taxid NCBI_accession SLV_taxonomy SLV_organisms_name SLV_taxid
AX664486 7227 AX664486 Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera; Drosophila melanogaster (fruit fly) 47180
BD307583 37089 BD307583 Eukaryota;SAR;Alveolata;Apicomplexa;Conoidasida;Coccidia;Eimeriorina;Toxoplasma; Neospora sp. 8805
BD359735 5858 BD359735 Eukaryota;SAR;Alveolata;Apicomplexa;Aconoidasida;Haemosporoidia;Plasmodium;Plasmodium malariae 8775
BD359736 5858 BD359736 Eukaryota;SAR;Alveolata;Apicomplexa;Aconoidasida;Haemosporoidia;Plasmodium;Plasmodium malariae 8775
CS214259 10116 CS214259 Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Deuterostomia;Chordata;Vertebrata;Gnathostomata;Euteleostomi;Tetrapoda;Mammalia; Rattus norvegicus (Norway rat) 47087
CS214261 10116 CS214261 Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Deuterostomia;Chordata;Vertebrata;Gnathostomata;Euteleostomi;Tetrapoda;Mammalia; Rattus norvegicus (Norway rat) 47087
CS214263 10116 CS214263 Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Deuterostomia;Chordata;Vertebrata;Gnathostomata;Euteleostomi;Tetrapoda;Mammalia; Rattus norvegicus (Norway rat) 47087
AB000106 28214 AB000106 Bacteria;Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sphingobium; Sphingomonas sp. 2850
AB000278 56192 AB000278 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Photobacterium; Photobacterium iliopiscarium 3781