GTDB-Tk v2: memory friendly classification with the genome taxonomy database
The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits...
Uloženo v:
| Vydáno v: | Bioinformatics (Oxford, England) Ročník 38; číslo 23; s. 5315 - 5316 |
|---|---|
| Hlavní autoři: | , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
England
Oxford University Press
30.11.2022
|
| Témata: | |
| ISSN: | 1367-4803, 1367-4811, 1367-4811 |
| On-line přístup: | Získat plný text |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification.
GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk.
Supplementary data are available at Bioinformatics online. |
|---|---|
| AbstractList | The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification.SUMMARYThe Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification.GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk.AVAILABILITY AND IMPLEMENTATIONGTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification. GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. Supplementary data are available at Bioinformatics online. |
| Author | Mussig, Aaron J Hugenholtz, Philip Parks, Donovan H Chaumeil, Pierre-Alain |
| Author_xml | – sequence: 1 givenname: Pierre-Alain orcidid: 0000-0003-0426-8445 surname: Chaumeil fullname: Chaumeil, Pierre-Alain – sequence: 2 givenname: Aaron J orcidid: 0000-0002-9988-0866 surname: Mussig fullname: Mussig, Aaron J – sequence: 3 givenname: Philip surname: Hugenholtz fullname: Hugenholtz, Philip – sequence: 4 givenname: Donovan H orcidid: 0000-0001-6662-9010 surname: Parks fullname: Parks, Donovan H |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36218463$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFkUtPHDEQhC1ExCv8BeRjLgN-zSuKIgUIm0grcdmcrbanhzWZsYntBfbfM2EXFHLh1C11VX1S1yHZ9cEjISecnXLWyjPjgvN9iCNkZ9OZyWCrWuyQAy6rulAN57uvO5P75DClW8ZYycpqj-zLSvBGVfKAzGeLy_Ni8Zvei890xDHENe2jQ98Na2oHSMn1zk6Q4OmDy0ual0hv0IcRaYbHMC1r2kEGAwk_kg89DAmPt_OI_Lr6vrj4UcyvZz8vvs0Lq7jKhRFMQQu9tD1iKTsEzhppyhbBKIumVsBKJYXqLKiuEzWolrVNJ40Q2DKUR-TrJvduZUbsLPocYdB30Y0Q1zqA028v3i31TbjXbc1ZWYop4NM2IIY_K0xZjy5ZHAbwGFZJi1rIhpdtU03Sk39Zr5CXF06CLxuBjSGliL22Lj8_bEK7QXOm_zam3zamt41N9uo_-wvhHeMTrRKlJA |
| CitedBy_id | crossref_primary_10_1038_s41467_024_52097_9 crossref_primary_10_1128_mra_00728_25 crossref_primary_10_1186_s40793_024_00616_y crossref_primary_10_1038_s41467_025_63401_6 crossref_primary_10_1007_s00284_024_04046_4 crossref_primary_10_1016_j_cels_2024_12_008 crossref_primary_10_1128_msystems_00710_25 crossref_primary_10_1007_s00203_023_03616_7 crossref_primary_10_1093_femsml_uqae027 crossref_primary_10_1016_j_marpolbul_2023_115557 crossref_primary_10_1186_s40168_024_01902_0 crossref_primary_10_1016_j_scitotenv_2024_176348 crossref_primary_10_1128_mra_00419_25 crossref_primary_10_1186_s13059_024_03471_9 crossref_primary_10_1016_j_copbio_2025_103266 crossref_primary_10_1093_femsml_uqae011 crossref_primary_10_3390_antibiotics14010080 crossref_primary_10_1128_spectrum_01983_24 crossref_primary_10_1128_msystems_00367_25 crossref_primary_10_3389_fmicb_2023_1199085 crossref_primary_10_1016_j_meegid_2024_105669 crossref_primary_10_1038_s41522_024_00522_8 crossref_primary_10_1128_msystems_00537_24 crossref_primary_10_1007_s12088_025_01524_6 crossref_primary_10_1038_s41597_024_02939_4 crossref_primary_10_3389_fmicb_2024_1523074 crossref_primary_10_1093_pcp_pcae011 crossref_primary_10_1128_mra_00454_24 crossref_primary_10_1186_s40168_025_02053_6 crossref_primary_10_1128_MRA_00844_23 crossref_primary_10_1007_s10482_025_02152_2 crossref_primary_10_1016_j_watres_2025_123188 crossref_primary_10_1016_j_tibtech_2024_08_013 crossref_primary_10_1186_s40168_023_01568_0 crossref_primary_10_12688_wellcomeopenres_24014_1 crossref_primary_10_1128_MRA_00910_23 crossref_primary_10_1371_journal_pone_0330523 crossref_primary_10_1016_j_fm_2025_104733 crossref_primary_10_1093_jimb_kuad042 crossref_primary_10_1128_mra_01274_22 crossref_primary_10_1016_j_cell_2024_12_036 crossref_primary_10_1029_2024JG008104 crossref_primary_10_1371_journal_pbio_3002787 crossref_primary_10_1021_acs_est_4c07554 crossref_primary_10_1002_imo2_70000 crossref_primary_10_1038_s41467_025_60699_0 crossref_primary_10_1128_aem_02502_24 crossref_primary_10_1111_gcb_70390 crossref_primary_10_1093_molbev_msae151 crossref_primary_10_1101_gr_278232_123 crossref_primary_10_3390_cancers17010070 crossref_primary_10_1007_s10482_024_02046_9 crossref_primary_10_1128_mra_01013_24 crossref_primary_10_1007_s00284_024_03921_4 crossref_primary_10_1186_s40793_024_00658_2 crossref_primary_10_1128_aem_01581_23 crossref_primary_10_1128_spectrum_00715_25 crossref_primary_10_1038_s41467_025_60390_4 crossref_primary_10_1371_journal_pcbi_1012343 crossref_primary_10_1016_j_jare_2024_09_016 crossref_primary_10_1038_s41467_024_47646_1 crossref_primary_10_1016_j_biortech_2025_132620 crossref_primary_10_3390_microorganisms11112819 crossref_primary_10_1007_s11274_024_04174_w crossref_primary_10_1186_s12864_024_10618_2 crossref_primary_10_1007_s10482_025_02078_9 crossref_primary_10_1128_spectrum_00541_24 crossref_primary_10_1093_jimb_kuad024 crossref_primary_10_1128_msystems_00999_24 crossref_primary_10_1016_j_jhazmat_2025_137870 crossref_primary_10_1128_spectrum_04021_23 crossref_primary_10_3389_fmicb_2024_1424368 crossref_primary_10_1007_s00284_025_04422_8 crossref_primary_10_1093_ismejo_wraf069 crossref_primary_10_1016_j_biortech_2025_132836 crossref_primary_10_1186_s13059_025_03524_7 crossref_primary_10_3390_microorganisms12122628 crossref_primary_10_1186_s40168_025_02051_8 crossref_primary_10_1016_j_xgen_2025_100949 crossref_primary_10_1186_s40168_025_02173_z crossref_primary_10_1038_s41467_025_63162_2 crossref_primary_10_1093_femsle_fnad071 crossref_primary_10_1093_ismejo_wraf058 crossref_primary_10_1093_jac_dkaf224 crossref_primary_10_1128_mra_01070_24 crossref_primary_10_1016_j_celrep_2024_114078 crossref_primary_10_3389_fmicb_2024_1343227 crossref_primary_10_1016_j_biortech_2024_131854 crossref_primary_10_1038_s41396_023_01392_2 crossref_primary_10_1111_1462_2920_16307 crossref_primary_10_3389_fmicb_2023_1226166 crossref_primary_10_1093_nar_gkae966 crossref_primary_10_3390_microorganisms12112252 crossref_primary_10_1093_ismeco_ycad011 crossref_primary_10_1016_j_syapm_2024_126500 crossref_primary_10_1093_ismeco_ycae102 crossref_primary_10_1016_j_watres_2025_124401 crossref_primary_10_1099_ijsem_0_006807 crossref_primary_10_1093_ismeco_ycae107 crossref_primary_10_1186_s12866_025_04115_z crossref_primary_10_1099_ijsem_0_006802 crossref_primary_10_1007_s12275_023_00064_2 crossref_primary_10_1038_s41467_023_41209_6 crossref_primary_10_1038_s41592_023_02025_4 crossref_primary_10_1093_ismejo_wrae197 crossref_primary_10_1186_s40168_024_01917_7 crossref_primary_10_1128_msystems_00175_25 crossref_primary_10_3389_fpls_2023_1259853 crossref_primary_10_1111_1462_2920_16541 crossref_primary_10_3389_fmicb_2025_1535420 crossref_primary_10_1038_s41467_024_52598_7 crossref_primary_10_1186_s12866_025_03834_7 crossref_primary_10_1093_ismejo_wraf049 crossref_primary_10_1128_mra_00989_23 crossref_primary_10_1016_j_syapm_2023_126452 crossref_primary_10_12688_wellcomeopenres_24165_1 crossref_primary_10_1099_ijsem_0_005951 crossref_primary_10_1016_j_ibiod_2024_105748 crossref_primary_10_1038_s41522_025_00746_2 crossref_primary_10_1111_1462_2920_70066 crossref_primary_10_1111_1462_2920_70067 crossref_primary_10_1016_j_watres_2025_123563 crossref_primary_10_1093_ismejo_wraf035 crossref_primary_10_1016_j_syapm_2024_126504 crossref_primary_10_1016_j_ygeno_2023_110742 crossref_primary_10_1128_aem_01250_23 crossref_primary_10_1016_j_dib_2025_111671 crossref_primary_10_1038_s41561_025_01768_3 crossref_primary_10_3389_fmicb_2024_1485353 crossref_primary_10_1007_s12275_024_00187_0 crossref_primary_10_1016_j_scitotenv_2024_174531 crossref_primary_10_1016_j_syapm_2024_126522 crossref_primary_10_1016_j_jenvman_2025_125756 crossref_primary_10_1099_mgen_0_001289 crossref_primary_10_12688_wellcomeopenres_24154_1 crossref_primary_10_1038_s41522_023_00399_z crossref_primary_10_1093_gigascience_giaf102 crossref_primary_10_1016_j_syapm_2024_126516 crossref_primary_10_3390_pathogens13121063 crossref_primary_10_1007_s10482_025_02145_1 crossref_primary_10_1016_j_jenvman_2024_123063 crossref_primary_10_1016_j_watres_2025_123589 crossref_primary_10_1128_mra_00496_25 crossref_primary_10_1093_ismeco_ycae113 crossref_primary_10_1021_acs_est_5c04981 crossref_primary_10_1128_msystems_01290_23 crossref_primary_10_1128_mra_00417_25 crossref_primary_10_1016_j_envres_2025_122241 crossref_primary_10_1038_s43247_025_02381_3 crossref_primary_10_1093_nsr_nwae378 crossref_primary_10_1099_mgen_0_001061 crossref_primary_10_12688_wellcomeopenres_23917_1 crossref_primary_10_1111_1462_2920_70083 crossref_primary_10_3389_fmicb_2025_1620548 crossref_primary_10_1128_aem_00022_25 crossref_primary_10_1093_ismejo_wraf014 crossref_primary_10_1016_j_syapm_2024_126525 crossref_primary_10_3389_fmicb_2023_1138751 crossref_primary_10_1016_j_fm_2023_104334 crossref_primary_10_1093_ismeco_ycae147 crossref_primary_10_1186_s13073_024_01306_7 crossref_primary_10_1128_aem_02099_23 crossref_primary_10_1093_nar_gkae528 crossref_primary_10_1093_ismeco_ycae143 crossref_primary_10_3389_fmicb_2025_1546594 crossref_primary_10_1128_spectrum_02355_24 crossref_primary_10_1099_ijsem_0_006846 crossref_primary_10_1099_ijsem_0_006610 crossref_primary_10_1111_1462_2920_70032 crossref_primary_10_1038_s41467_024_51062_w crossref_primary_10_1111_1462_2920_70036 crossref_primary_10_3390_diagnostics14121274 crossref_primary_10_1093_ismejo_wraf001 crossref_primary_10_1002_imt2_70002 crossref_primary_10_1186_s42523_024_00364_x crossref_primary_10_1128_msystems_01571_24 crossref_primary_10_1038_s41597_024_04315_8 crossref_primary_10_1186_s13099_024_00662_4 crossref_primary_10_1099_ijsem_0_006843 crossref_primary_10_3390_pathogens12111345 crossref_primary_10_1186_s40168_023_01679_8 crossref_primary_10_1021_acs_jafc_5c03309 crossref_primary_10_3389_fmicb_2023_1114548 crossref_primary_10_1111_1462_2920_70024 crossref_primary_10_3389_fmicb_2025_1588169 crossref_primary_10_1093_ismejo_wrae147 crossref_primary_10_1038_s44222_025_00346_x crossref_primary_10_1038_s41597_025_05230_2 crossref_primary_10_1080_19490976_2024_2446374 crossref_primary_10_1128_spectrum_00917_25 crossref_primary_10_1111_gcb_70329 crossref_primary_10_1099_mgen_0_001489 crossref_primary_10_1128_aem_02229_24 crossref_primary_10_1099_ijsem_0_006633 crossref_primary_10_3390_ijms25021090 crossref_primary_10_1038_s41467_024_54025_3 crossref_primary_10_1111_1462_2920_70054 crossref_primary_10_1093_femsec_fiad122 crossref_primary_10_1093_ismeco_ycaf022 crossref_primary_10_1093_ismeco_ycaf021 crossref_primary_10_1073_pnas_2501422122 crossref_primary_10_1186_s13059_024_03216_8 crossref_primary_10_1093_ismejo_wrae129 crossref_primary_10_1093_nar_gkaf606 crossref_primary_10_1186_s12859_024_06030_y crossref_primary_10_1038_s41467_023_44290_z crossref_primary_10_1016_j_chom_2024_02_003 crossref_primary_10_1099_acmi_0_000646_v6 crossref_primary_10_1111_mpp_70019 crossref_primary_10_1099_ijsem_0_006857 crossref_primary_10_1093_gbe_evaf128 crossref_primary_10_1016_j_idairyj_2024_106160 crossref_primary_10_1016_j_jenvman_2025_125575 crossref_primary_10_1093_nar_gkae523 crossref_primary_10_1093_ismejo_wrad033 crossref_primary_10_1128_msystems_01280_22 crossref_primary_10_1186_s40168_025_02153_3 crossref_primary_10_1186_s12866_025_03823_w crossref_primary_10_1038_s41467_024_49958_8 crossref_primary_10_1089_cmb_2024_0663 crossref_primary_10_1128_aem_02108_22 crossref_primary_10_3389_fmicb_2024_1487595 crossref_primary_10_1093_nar_gkaf659 crossref_primary_10_1099_mgen_0_001305 crossref_primary_10_1016_j_syapm_2025_126622 crossref_primary_10_12688_wellcomeopenres_24281_1 crossref_primary_10_1007_s13205_025_04464_6 crossref_primary_10_1016_j_ecoenv_2024_117204 crossref_primary_10_1016_j_syapm_2025_126621 crossref_primary_10_1007_s00248_024_02442_8 crossref_primary_10_1099_ijsem_0_006409 crossref_primary_10_1038_s41467_023_37396_x crossref_primary_10_1128_msystems_01091_25 crossref_primary_10_1099_ijsem_0_006411 crossref_primary_10_1128_mra_00459_24 crossref_primary_10_1093_ismeco_ycaf042 crossref_primary_10_1038_s43247_025_02637_y crossref_primary_10_3390_microorganisms12040707 crossref_primary_10_1128_mra_01040_23 crossref_primary_10_1128_spectrum_02832_23 crossref_primary_10_1099_ijsem_0_005793 crossref_primary_10_1099_ijsem_0_006641 crossref_primary_10_1038_s41467_024_51346_1 crossref_primary_10_1038_s42003_024_06825_y crossref_primary_10_1016_j_foodres_2025_117259 crossref_primary_10_1016_j_syapm_2025_126606 crossref_primary_10_1016_j_aquaculture_2024_741913 crossref_primary_10_1016_j_jhazmat_2025_139293 crossref_primary_10_1080_19490976_2023_2298254 crossref_primary_10_1186_s40168_024_01830_z crossref_primary_10_1016_j_ijhydene_2025_150246 crossref_primary_10_12688_wellcomeopenres_24400_1 crossref_primary_10_1038_s41597_024_04118_x crossref_primary_10_1093_ismejo_wrae215 crossref_primary_10_1007_s00284_025_04257_3 crossref_primary_10_12688_wellcomeopenres_24087_1 crossref_primary_10_1016_j_chom_2024_10_017 crossref_primary_10_1128_mra_01281_24 crossref_primary_10_1038_s41467_025_56077_5 crossref_primary_10_1093_femsec_fiae117 crossref_primary_10_1016_j_watres_2025_123621 crossref_primary_10_1126_science_adn0953 crossref_primary_10_1038_s41598_024_56603_3 crossref_primary_10_1073_pnas_2424463122 crossref_primary_10_1016_j_jare_2025_09_019 crossref_primary_10_1111_1758_2229_70188 crossref_primary_10_1128_msystems_00027_25 crossref_primary_10_1128_msystems_01366_24 crossref_primary_10_1128_msphere_00367_25 crossref_primary_10_12688_wellcomeopenres_24098_1 crossref_primary_10_1016_j_ympev_2025_108321 crossref_primary_10_1186_s12864_023_09644_3 crossref_primary_10_1007_s00203_024_03937_1 crossref_primary_10_1016_j_syapm_2024_126541 crossref_primary_10_1099_mgen_0_001503 crossref_primary_10_1038_s41467_024_55222_w crossref_primary_10_1111_1751_7915_70107 crossref_primary_10_1016_j_margen_2024_101125 crossref_primary_10_1093_nar_gkad282 crossref_primary_10_1128_msphere_00607_23 crossref_primary_10_1093_gigascience_giad022 crossref_primary_10_1038_s41587_025_02810_w crossref_primary_10_1186_s13073_025_01500_1 crossref_primary_10_1038_s41467_024_45895_8 crossref_primary_10_1016_j_syapm_2025_126650 crossref_primary_10_1016_j_syapm_2025_126652 crossref_primary_10_1038_s41467_025_59558_9 crossref_primary_10_1016_j_jenvman_2025_124858 crossref_primary_10_1038_s41467_025_61302_2 crossref_primary_10_1016_j_jhazmat_2024_135821 crossref_primary_10_1073_pnas_2416761121 crossref_primary_10_1016_j_syapm_2025_126648 crossref_primary_10_1099_ijsem_0_006440 crossref_primary_10_1016_j_cej_2023_146782 crossref_primary_10_1016_j_syapm_2025_126640 crossref_primary_10_1016_j_syapm_2024_126562 crossref_primary_10_1093_femsec_fiaf018 crossref_primary_10_1016_j_syapm_2025_126643 crossref_primary_10_1038_s41564_023_01593_7 crossref_primary_10_1016_j_jhazmat_2025_139250 crossref_primary_10_1016_j_algal_2025_104256 crossref_primary_10_1128_jcm_00860_25 crossref_primary_10_1016_j_hal_2025_102956 crossref_primary_10_3390_microorganisms13020222 crossref_primary_10_1099_ijsem_0_006474 crossref_primary_10_1007_s10482_024_01950_4 crossref_primary_10_26508_lsa_202302480 crossref_primary_10_1038_s41586_024_07960_6 crossref_primary_10_1016_j_syapm_2024_126559 crossref_primary_10_1186_s13062_025_00680_5 crossref_primary_10_1016_j_syapm_2025_126639 crossref_primary_10_1186_s40168_024_01952_4 crossref_primary_10_3168_jds_2025_26662 crossref_primary_10_1002_imt2_70061 crossref_primary_10_1038_s41587_023_01983_6 crossref_primary_10_1016_j_syapm_2024_126575 crossref_primary_10_1016_j_ijantimicag_2024_107382 crossref_primary_10_1016_j_ijhydene_2023_08_017 crossref_primary_10_1038_s41467_024_46459_6 crossref_primary_10_1016_j_dib_2024_110655 crossref_primary_10_1371_journal_pone_0326734 crossref_primary_10_1016_j_watres_2025_124515 crossref_primary_10_12688_wellcomeopenres_24187_1 crossref_primary_10_3389_fmicb_2025_1557188 crossref_primary_10_1038_s41522_024_00597_3 crossref_primary_10_1016_j_syapm_2025_126623 crossref_primary_10_1016_j_syapm_2025_126625 crossref_primary_10_1016_j_syapm_2025_126629 crossref_primary_10_1016_j_watres_2024_122863 crossref_primary_10_1016_j_jhazmat_2023_133333 crossref_primary_10_3389_fmicb_2023_1109549 crossref_primary_10_1099_ijsem_0_006499 crossref_primary_10_1128_mra_00445_25 crossref_primary_10_1126_science_adr8286 crossref_primary_10_1016_j_aquatox_2024_106925 crossref_primary_10_1111_jpy_13523 crossref_primary_10_1186_s40793_025_00690_w crossref_primary_10_1016_j_cell_2025_01_039 crossref_primary_10_3389_fmicb_2025_1662087 crossref_primary_10_3390_ani15131998 crossref_primary_10_1111_jpy_13533 crossref_primary_10_1016_j_ajt_2023_06_011 crossref_primary_10_1186_s13059_023_03090_w crossref_primary_10_1016_j_watres_2024_122887 crossref_primary_10_1038_s41564_024_01804_9 crossref_primary_10_1099_acmi_0_000931_v4 crossref_primary_10_3390_microorganisms12010005 crossref_primary_10_1128_mra_00457_24 crossref_primary_10_1186_s42523_025_00453_5 crossref_primary_10_3389_fmicb_2024_1523912 crossref_primary_10_1093_bioadv_vbad060 crossref_primary_10_1007_s10201_025_00815_7 crossref_primary_10_1002_ccr3_70103 crossref_primary_10_1007_s10482_024_01994_6 crossref_primary_10_3389_fevo_2023_1205557 crossref_primary_10_1186_s40793_024_00549_6 crossref_primary_10_1007_s00300_025_03367_9 crossref_primary_10_1128_msystems_01007_24 crossref_primary_10_1093_femsec_fiaf051 crossref_primary_10_12688_wellcomeopenres_24744_1 crossref_primary_10_1016_j_ese_2025_100560 crossref_primary_10_1038_s41467_024_53670_y crossref_primary_10_1016_j_cej_2025_166596 crossref_primary_10_1038_s41592_024_02262_1 crossref_primary_10_1080_19490976_2025_2501192 crossref_primary_10_1186_s40104_025_01183_z crossref_primary_10_1038_s41587_025_02738_1 crossref_primary_10_1093_bib_bbae680 crossref_primary_10_1371_journal_pntd_0013016 crossref_primary_10_3390_md23080316 crossref_primary_10_1093_nargab_lqaf083 crossref_primary_10_1128_mra_00715_24 crossref_primary_10_1038_s41522_024_00588_4 crossref_primary_10_1128_mra_00403_24 crossref_primary_10_1016_j_ebiom_2024_105516 crossref_primary_10_7717_peerj_16513 crossref_primary_10_3390_microorganisms12010016 crossref_primary_10_1016_j_chemosphere_2025_144285 crossref_primary_10_3389_fmicb_2024_1338026 crossref_primary_10_1139_gen_2023_0099 crossref_primary_10_12688_wellcomeopenres_24799_1 crossref_primary_10_1128_mra_00190_25 crossref_primary_10_1038_s41598_024_56480_w crossref_primary_10_1099_ijsem_0_006288 crossref_primary_10_1080_19490976_2025_2516699 crossref_primary_10_3389_fmicb_2023_1288286 crossref_primary_10_1016_j_phrs_2024_107385 crossref_primary_10_1128_mra_01121_24 crossref_primary_10_1016_j_envres_2024_119788 crossref_primary_10_1016_j_watres_2024_122208 crossref_primary_10_12688_wellcomeopenres_24304_1 crossref_primary_10_1002_imo2_56 crossref_primary_10_1016_j_chom_2025_08_008 crossref_primary_10_1016_j_watres_2023_121030 crossref_primary_10_1016_j_biortech_2024_131046 crossref_primary_10_1016_j_scitotenv_2025_179519 crossref_primary_10_1186_s40168_024_01956_0 crossref_primary_10_3389_fmicb_2023_1281628 crossref_primary_10_3390_microorganisms13081888 crossref_primary_10_1128_mra_00899_24 crossref_primary_10_1093_nargab_lqaf093 crossref_primary_10_1016_j_scitotenv_2025_179522 crossref_primary_10_1038_s41467_024_45257_4 crossref_primary_10_1128_MRA_00667_23 crossref_primary_10_1099_acmi_0_000910_v3 crossref_primary_10_1038_s41396_023_01516_8 crossref_primary_10_1186_s12864_025_11410_6 crossref_primary_10_1094_PHYTO_10_24_0321_R crossref_primary_10_1016_j_jhazmat_2025_138862 crossref_primary_10_1128_mra_00029_25 crossref_primary_10_3389_fcimb_2024_1361432 crossref_primary_10_1002_mbo3_70004 crossref_primary_10_1128_mra_00866_24 crossref_primary_10_1016_j_celrep_2024_115018 crossref_primary_10_3390_microorganisms11122932 crossref_primary_10_1016_j_micres_2025_128299 crossref_primary_10_1016_j_envpol_2025_126144 crossref_primary_10_1002_imt2_201 crossref_primary_10_1093_gigascience_giaf081 crossref_primary_10_1016_j_envint_2024_108920 crossref_primary_10_1186_s40168_024_01903_z crossref_primary_10_1128_mra_00385_25 crossref_primary_10_1186_s12864_024_10594_7 crossref_primary_10_1016_j_alcohol_2024_01_006 crossref_primary_10_1080_19490976_2024_2407047 crossref_primary_10_1134_S002626172260327X crossref_primary_10_1093_gigascience_giaf072 crossref_primary_10_1016_j_algal_2024_103569 crossref_primary_10_1016_j_envres_2023_115866 crossref_primary_10_3389_fmicb_2022_1095497 crossref_primary_10_3389_fmicb_2024_1407904 crossref_primary_10_1093_bib_bbae419 crossref_primary_10_1134_S0026261723603949 crossref_primary_10_1007_s00284_024_03815_5 crossref_primary_10_1080_03079457_2025_2552314 crossref_primary_10_1038_s41467_024_47523_x crossref_primary_10_3389_fcimb_2025_1647377 crossref_primary_10_1016_j_envint_2024_108946 crossref_primary_10_1016_j_jece_2024_113314 crossref_primary_10_1093_gigascience_giaf062 crossref_primary_10_3389_fpls_2024_1437947 crossref_primary_10_1038_s44221_025_00430_x crossref_primary_10_1016_j_ibiod_2024_105806 crossref_primary_10_1093_nar_gkae1004 crossref_primary_10_1111_jpy_13392 crossref_primary_10_1007_s00203_025_04375_3 crossref_primary_10_1128_mbio_03843_24 crossref_primary_10_1128_mra_00295_25 crossref_primary_10_3389_fmicb_2025_1648896 crossref_primary_10_1186_s40168_024_02026_1 crossref_primary_10_3389_fmicb_2025_1649750 crossref_primary_10_1128_msystems_00342_25 crossref_primary_10_1016_j_jwpe_2025_108395 crossref_primary_10_1016_j_envres_2025_121603 crossref_primary_10_1016_j_micres_2025_128086 crossref_primary_10_1080_1040841X_2024_2306465 crossref_primary_10_3390_md23090362 crossref_primary_10_1016_j_isci_2024_109211 crossref_primary_10_3390_v16040590 crossref_primary_10_1016_j_ygeno_2025_111089 crossref_primary_10_1038_s41467_024_53784_3 crossref_primary_10_1093_nar_gkad964 crossref_primary_10_1371_journal_pbio_3002897 crossref_primary_10_3390_v17050623 crossref_primary_10_1002_imt2_244 crossref_primary_10_1016_j_scitotenv_2024_177594 crossref_primary_10_1016_j_csbj_2023_12_025 crossref_primary_10_1134_S0026261724606833 crossref_primary_10_1002_ece3_71910 crossref_primary_10_1016_j_sjbs_2024_103957 crossref_primary_10_1016_j_watres_2025_124178 crossref_primary_10_1186_s40168_024_01807_y crossref_primary_10_1016_j_scitotenv_2025_179827 crossref_primary_10_3389_fpls_2025_1664284 crossref_primary_10_3389_fmicb_2023_1125709 crossref_primary_10_3389_fmicb_2024_1379500 crossref_primary_10_1093_bib_bbae620 crossref_primary_10_1128_mra_00934_22 crossref_primary_10_1186_s40793_025_00689_3 crossref_primary_10_1128_mra_00268_25 crossref_primary_10_1128_spectrum_03590_23 crossref_primary_10_1007_s00203_023_03737_z crossref_primary_10_1021_acs_est_4c09839 crossref_primary_10_1038_s41467_024_49602_5 crossref_primary_10_1038_s41598_024_72329_8 crossref_primary_10_1093_nar_gkad943 crossref_primary_10_3389_fmicb_2024_1356891 crossref_primary_10_1016_j_ibiod_2024_105846 crossref_primary_10_1016_j_chom_2023_03_010 crossref_primary_10_3390_microorganisms13092005 crossref_primary_10_1186_s42523_025_00409_9 crossref_primary_10_1007_s00253_023_12991_6 crossref_primary_10_3390_ijms242317105 crossref_primary_10_1111_1462_2920_16669 crossref_primary_10_3389_fmicb_2023_1203164 crossref_primary_10_1128_mra_00210_23 crossref_primary_10_1016_j_fm_2025_104819 crossref_primary_10_1093_nar_gkae609 crossref_primary_10_1186_s40168_024_01786_0 crossref_primary_10_1093_ismejo_wraf165 crossref_primary_10_1093_gigascience_giaf004 crossref_primary_10_1038_s41467_025_61432_7 crossref_primary_10_3389_fmicb_2024_1361883 crossref_primary_10_1016_j_biortech_2024_130413 crossref_primary_10_3389_fmicb_2024_1414000 crossref_primary_10_1038_s41467_023_39508_z crossref_primary_10_3390_w17010052 crossref_primary_10_1016_j_envres_2025_122108 crossref_primary_10_3390_ijms26041713 crossref_primary_10_1099_ijsem_0_006914 crossref_primary_10_1264_jsme2_ME24067 crossref_primary_10_1099_ijsem_0_006920 crossref_primary_10_1016_j_cej_2024_151390 crossref_primary_10_1021_acs_est_4c05624 crossref_primary_10_1093_ismejo_wraf153 crossref_primary_10_1128_MRA_00651_23 crossref_primary_10_1111_1755_0998_70042 crossref_primary_10_3390_fermentation9080719 crossref_primary_10_1186_s40168_025_02156_0 crossref_primary_10_1016_j_cmet_2024_12_010 crossref_primary_10_3389_fmicb_2023_1254535 crossref_primary_10_1016_j_watres_2025_123699 crossref_primary_10_1099_ijsem_0_006708 crossref_primary_10_1099_ijsem_0_006705 crossref_primary_10_1016_j_jhazmat_2024_135493 crossref_primary_10_1016_j_watres_2025_124308 crossref_primary_10_1099_mgen_0_001167 crossref_primary_10_1038_s41538_024_00269_8 crossref_primary_10_1128_mra_00485_25 crossref_primary_10_1016_j_jhazmat_2024_136587 crossref_primary_10_1016_j_jhazmat_2024_135017 crossref_primary_10_1093_ismejo_wrae057 crossref_primary_10_1016_j_marpolbul_2024_116651 crossref_primary_10_1016_j_watres_2025_123450 crossref_primary_10_1093_molbev_msaf181 crossref_primary_10_1038_s41467_024_52771_y crossref_primary_10_1038_s41522_025_00649_2 crossref_primary_10_3389_fmicb_2024_1441865 crossref_primary_10_12688_f1000research_152290_2 crossref_primary_10_12688_f1000research_152290_1 crossref_primary_10_1186_s12866_025_04149_3 crossref_primary_10_12688_wellcomeopenres_24166_1 crossref_primary_10_1038_s41396_023_01547_1 crossref_primary_10_1038_s41522_025_00747_1 crossref_primary_10_1038_s43705_023_00254_4 crossref_primary_10_1038_s41467_025_58280_w crossref_primary_10_1016_j_ecoenv_2025_118063 crossref_primary_10_1038_s41467_024_53446_4 crossref_primary_10_1093_ismejo_wraf138 crossref_primary_10_3389_fmicb_2025_1533115 crossref_primary_10_1128_msystems_00422_25 crossref_primary_10_1128_mra_00988_23 crossref_primary_10_7717_peerj_18023 crossref_primary_10_1099_mgen_0_001101 crossref_primary_10_1111_1462_2920_70154 crossref_primary_10_3390_ani14243625 crossref_primary_10_1371_journal_pgen_1011295 crossref_primary_10_1093_ismejo_wraf126 crossref_primary_10_1016_j_gca_2024_04_019 crossref_primary_10_3390_biology14091271 crossref_primary_10_1093_ismejo_wraf119 crossref_primary_10_1093_ismeco_ycaf101 crossref_primary_10_3390_life14050563 crossref_primary_10_1038_s42003_024_06535_5 crossref_primary_10_1038_s42003_023_05695_0 crossref_primary_10_1099_mgen_0_001351 crossref_primary_10_1007_s00792_024_01342_6 crossref_primary_10_1099_ijsem_0_006721 crossref_primary_10_1128_mra_00710_23 crossref_primary_10_1007_s00203_024_03896_7 crossref_primary_10_1038_s41396_023_01491_0 crossref_primary_10_1093_ismejo_wrae260 crossref_primary_10_1093_gbe_evaf022 crossref_primary_10_1093_ismejo_wraf117 crossref_primary_10_1093_ismejo_wraf108 crossref_primary_10_1128_spectrum_01775_23 crossref_primary_10_1128_msystems_01291_24 crossref_primary_10_1128_mra_01022_23 crossref_primary_10_1021_acs_est_5c03342 crossref_primary_10_12688_wellcomeopenres_24738_1 crossref_primary_10_3389_fmicb_2024_1452795 crossref_primary_10_1016_j_scitotenv_2023_166799 crossref_primary_10_1111_1462_2920_70178 crossref_primary_10_1038_s43247_025_02610_9 crossref_primary_10_1038_s41598_024_56870_0 crossref_primary_10_1128_mra_00722_25 crossref_primary_10_1016_j_cell_2025_05_034 crossref_primary_10_1038_s41598_025_05431_0 crossref_primary_10_1128_mbio_00749_25 crossref_primary_10_1038_s41467_025_61467_w crossref_primary_10_1007_s42770_024_01268_3 crossref_primary_10_1128_mbio_03595_24 crossref_primary_10_1099_ijsem_0_006735 crossref_primary_10_1099_mgen_0_001134 crossref_primary_10_1111_1462_2920_70163 crossref_primary_10_1093_ismejo_wrae240 crossref_primary_10_1186_s42523_025_00395_y crossref_primary_10_1371_journal_pbio_3003130 crossref_primary_10_3389_fmicb_2023_1229783 crossref_primary_10_1111_1462_2920_16696 crossref_primary_10_1186_s40168_024_01984_w crossref_primary_10_3390_microorganisms11030555 crossref_primary_10_1016_j_celrep_2024_114602 crossref_primary_10_1128_mbio_01231_25 crossref_primary_10_1038_s41598_024_61549_7 crossref_primary_10_1128_msystems_00200_25 crossref_primary_10_1099_mgen_0_001422 crossref_primary_10_1167_iovs_65_3_26 crossref_primary_10_1038_s41598_024_59279_x crossref_primary_10_1016_j_resmic_2024_104202 crossref_primary_10_1186_s12915_025_02129_7 crossref_primary_10_1099_ijsem_0_006769 crossref_primary_10_1111_1758_2229_13246 crossref_primary_10_1128_mra_00917_24 crossref_primary_10_1099_ijsem_0_006771 crossref_primary_10_1016_j_jhazmat_2024_135511 crossref_primary_10_1093_ismejo_wrae113 crossref_primary_10_1007_s10482_024_01997_3 crossref_primary_10_1093_ismejo_wrae111 crossref_primary_10_1093_ismejo_wrad022 crossref_primary_10_1016_j_watres_2024_122580 crossref_primary_10_1093_ismejo_wrae116 crossref_primary_10_1093_ismejo_wrae115 crossref_primary_10_1093_ismejo_wrae109 crossref_primary_10_1099_ijsem_0_006515 crossref_primary_10_1128_aem_00570_23 crossref_primary_10_1016_j_dib_2025_111748 crossref_primary_10_1007_s00284_024_03657_1 crossref_primary_10_1093_ismejo_wrad011 crossref_primary_10_1128_MRA_00460_23 crossref_primary_10_1016_j_envint_2025_109769 crossref_primary_10_1099_mgen_0_001207 crossref_primary_10_3390_pathogens14050465 crossref_primary_10_1093_bioinformatics_btae452 crossref_primary_10_12688_wellcomeopenres_24173_1 crossref_primary_10_1093_nargab_lqae088 crossref_primary_10_1111_1462_2920_70010 crossref_primary_10_1099_ijsem_0_006550 crossref_primary_10_1021_jacs_5c08818 crossref_primary_10_3389_fgene_2024_1422274 crossref_primary_10_1038_s41591_024_02823_z crossref_primary_10_1038_s41586_025_08781_x crossref_primary_10_1016_j_envres_2024_120603 crossref_primary_10_1016_j_watres_2025_123503 crossref_primary_10_1038_s41467_025_62455_w crossref_primary_10_1038_s41564_025_02110_8 crossref_primary_10_1099_mgen_0_001456 crossref_primary_10_12688_wellcomeopenres_24798_1 crossref_primary_10_1016_j_envint_2024_109239 crossref_primary_10_3389_fgeoc_2024_1410338 crossref_primary_10_1016_j_apsoil_2025_106190 crossref_primary_10_1128_mra_00083_24 crossref_primary_10_1099_ijsem_0_006300 crossref_primary_10_12688_wellcomeopenres_24763_1 crossref_primary_10_1038_s41390_025_04386_2 crossref_primary_10_1111_1462_2920_70004 crossref_primary_10_1099_ijsem_0_006781 crossref_primary_10_1007_s42770_024_01566_w crossref_primary_10_1016_j_watres_2024_122590 crossref_primary_10_1038_s41467_024_54237_7 crossref_primary_10_1186_s12864_024_10610_w crossref_primary_10_1128_mra_00048_23 crossref_primary_10_1128_msphere_01002_24 crossref_primary_10_1038_s41597_025_05736_9 crossref_primary_10_1128_mra_00862_23 crossref_primary_10_12688_wellcomeopenres_23988_1 crossref_primary_10_1007_s10811_023_02986_1 crossref_primary_10_1038_s41597_024_03889_7 crossref_primary_10_1093_nar_gkaf340 crossref_primary_10_1128_spectrum_00492_24 crossref_primary_10_1016_j_crmicr_2025_100438 crossref_primary_10_3389_fbrio_2023_1275910 crossref_primary_10_1128_mra_00355_25 crossref_primary_10_1038_s41586_025_08955_7 crossref_primary_10_1016_j_biortech_2025_133045 crossref_primary_10_1016_j_crmicr_2025_100433 crossref_primary_10_1016_j_jece_2024_114269 crossref_primary_10_1128_msystems_01250_24 crossref_primary_10_1038_s42256_024_00908_5 crossref_primary_10_1093_bioinformatics_btaf334 crossref_primary_10_12688_wellcomeopenres_24186_1 crossref_primary_10_1128_mra_00549_24 crossref_primary_10_1128_mra_00824_24 crossref_primary_10_1093_bioadv_vbaf152 crossref_primary_10_1016_j_soilbio_2023_109279 crossref_primary_10_1128_msystems_00581_25 crossref_primary_10_12688_wellcomeopenres_24099_1 crossref_primary_10_1099_ijsem_0_006560 crossref_primary_10_1128_mra_00400_25 crossref_primary_10_1128_spectrum_03276_23 crossref_primary_10_3389_fmicb_2024_1301073 crossref_primary_10_3389_fmicb_2025_1437936 crossref_primary_10_1128_MRA_00620_23 crossref_primary_10_1038_s41538_025_00479_8 crossref_primary_10_1038_s41598_024_78564_3 crossref_primary_10_1099_ijsem_0_006359 crossref_primary_10_1128_mra_00608_24 crossref_primary_10_3389_fmicb_2024_1369263 crossref_primary_10_1111_1758_2229_70098 crossref_primary_10_1099_ijsem_0_006593 crossref_primary_10_1093_bib_bbaf267 crossref_primary_10_1038_s41586_024_07754_w crossref_primary_10_1016_j_jhazmat_2024_136811 crossref_primary_10_1099_ijsem_0_006346 crossref_primary_10_1128_mra_00846_24 crossref_primary_10_1093_femsec_fiae047 crossref_primary_10_1016_j_cell_2025_08_016 crossref_primary_10_3389_fmicb_2025_1597580 crossref_primary_10_1038_s41597_023_02222_y crossref_primary_10_1128_msphere_00192_24 crossref_primary_10_1371_journal_pone_0320639 crossref_primary_10_1186_s12866_025_04296_7 crossref_primary_10_1016_j_scitotenv_2025_178521 crossref_primary_10_1186_s40793_023_00518_5 crossref_primary_10_3389_fmicb_2025_1589971 crossref_primary_10_1007_s10811_025_03461_9 crossref_primary_10_3390_nu17020338 crossref_primary_10_1093_jacamr_dlaf140 crossref_primary_10_1016_j_algal_2024_103870 crossref_primary_10_1038_s41467_024_52669_9 crossref_primary_10_1099_ijsem_0_006369 crossref_primary_10_1007_s00284_025_04493_7 crossref_primary_10_12688_wellcomeopenres_24745_1 crossref_primary_10_1186_s40168_024_01922_w crossref_primary_10_1093_nar_gkaf397 crossref_primary_10_1016_j_cej_2025_166496 crossref_primary_10_1016_j_envint_2024_108555 crossref_primary_10_1038_s41559_024_02505_6 crossref_primary_10_1099_mic_0_001489 crossref_primary_10_1038_s41586_024_07495_w crossref_primary_10_1016_j_jmb_2023_168016 crossref_primary_10_1099_mgen_0_000995 crossref_primary_10_1128_aem_02420_24 crossref_primary_10_12688_f1000research_128091_2 crossref_primary_10_12688_f1000research_128091_1 crossref_primary_10_1016_j_scitotenv_2025_179831 crossref_primary_10_1016_j_ecoenv_2025_118991 crossref_primary_10_1038_s41564_025_02091_8 crossref_primary_10_1038_s41467_024_48498_5 crossref_primary_10_1590_0074_02760240156 crossref_primary_10_1128_mra_00284_24 crossref_primary_10_1038_s41586_024_08553_z crossref_primary_10_1186_s40793_025_00758_7 crossref_primary_10_1128_mbio_01555_25 crossref_primary_10_1016_j_nbt_2025_04_008 crossref_primary_10_3389_fmicb_2025_1535096 crossref_primary_10_1093_femsle_fnae089 crossref_primary_10_1128_mra_00205_23 crossref_primary_10_1016_j_cell_2025_08_020 crossref_primary_10_1080_22221751_2025_2528537 crossref_primary_10_1128_aem_00188_25 crossref_primary_10_3389_fmicb_2025_1614301 crossref_primary_10_1128_spectrum_00423_25 crossref_primary_10_1038_s41598_024_78066_2 crossref_primary_10_1016_j_micpath_2025_107610 crossref_primary_10_1093_nar_gkad196 crossref_primary_10_1038_s41597_025_05567_8 crossref_primary_10_1016_j_watres_2024_122302 crossref_primary_10_1016_j_cej_2024_149824 crossref_primary_10_1038_s41467_024_52996_x crossref_primary_10_1007_s10482_024_02030_3 crossref_primary_10_3389_fmicb_2023_1233691 crossref_primary_10_1128_mra_01085_24 crossref_primary_10_3390_w15193415 crossref_primary_10_3390_w17111574 crossref_primary_10_1038_s42003_024_06136_2 crossref_primary_10_1038_s41467_023_44636_7 crossref_primary_10_1038_s41598_025_06125_3 crossref_primary_10_1007_s00253_024_13346_5 crossref_primary_10_1128_msystems_00242_24 crossref_primary_10_1128_mbio_00941_25 crossref_primary_10_3389_fmicb_2023_1197329 crossref_primary_10_1186_s12864_025_11590_1 crossref_primary_10_1038_s41598_025_12132_1 crossref_primary_10_1093_femsre_fuae031 crossref_primary_10_1016_j_aquaculture_2023_740221 crossref_primary_10_1038_s43247_023_00796_4 crossref_primary_10_1016_j_chom_2024_06_005 crossref_primary_10_12688_wellcomeopenres_24743_1 crossref_primary_10_1016_j_chom_2024_06_002 crossref_primary_10_3389_fmicb_2023_1212538 crossref_primary_10_1038_s41598_024_80127_5 crossref_primary_10_1038_s41467_025_58769_4 crossref_primary_10_1016_j_chom_2023_11_015 crossref_primary_10_1093_jambio_lxaf179 crossref_primary_10_1128_aem_01164_25 crossref_primary_10_1038_s41597_024_03961_2 crossref_primary_10_1016_j_syapm_2025_126591 crossref_primary_10_3390_w17071061 crossref_primary_10_1128_mra_00458_24 crossref_primary_10_1371_journal_pone_0328194 crossref_primary_10_1128_mra_00716_23 crossref_primary_10_1186_s12915_025_02269_w crossref_primary_10_1038_s41429_024_00706_6 crossref_primary_10_1128_mra_00574_24 crossref_primary_10_3390_microorganisms11010168 |
| Cites_doi | 10.1038/s41587-020-0718-6 10.1038/s41587-020-0501-8 10.1186/1471-2105-11-538 10.1038/s41587-020-0603-3 10.1111/1755-0998.13527 10.1093/sysbio/syy054 10.1093/bioinformatics/btz848 10.1093/nar/gkab776 |
| ContentType | Journal Article |
| Copyright | The Author(s) 2022. Published by Oxford University Press. The Author(s) 2022. Published by Oxford University Press. 2022 |
| Copyright_xml | – notice: The Author(s) 2022. Published by Oxford University Press. – notice: The Author(s) 2022. Published by Oxford University Press. 2022 |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 5PM |
| DOI | 10.1093/bioinformatics/btac672 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic MEDLINE |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1367-4811 |
| EndPage | 5316 |
| ExternalDocumentID | PMC9710552 36218463 10_1093_bioinformatics_btac672 |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GrantInformation_xml | – fundername: UQ Strategic Funding and Australian Research Council Laureate Fellowship grantid: FL150100038 – fundername: ; grantid: FL150100038 |
| GroupedDBID | --- -E4 -~X .2P .DC .I3 0R~ 23N 2WC 4.4 48X 53G 5GY 5WA 70D AAIJN AAIMJ AAJKP AAKPC AAMDB AAMVS AAOGV AAPQZ AAPXW AAVAP AAVLN AAYXX ABEJV ABEUO ABGNP ABIXL ABNKS ABPTD ABQLI ABWST ABXVV ABZBJ ACGFS ACIWK ACPRK ACUFI ACYTK ADBBV ADEYI ADEZT ADFTL ADGZP ADHKW ADHZD ADMLS ADOCK ADPDF ADRTK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFZL AFIYH AFOFC AFRAH AGINJ AGKEF AGQXC AGSYK AHMBA AHXPO AIJHB AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC AMNDL APIBT APWMN ARIXL ASPBG AVWKF AXUDD AYOIW AZVOD BAWUL BAYMD BHONS BQDIO BQUQU BSWAC BTQHN C45 CDBKE CITATION CS3 CZ4 DAKXR DIK DILTD DU5 D~K EBD EBS EE~ EMOBN F5P F9B FEDTE FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GROUPED_DOAJ GX1 H13 H5~ HAR HW0 HZ~ IOX J21 JXSIZ KAQDR KOP KQ8 KSI KSN M-Z MK~ ML0 N9A NGC NLBLG NMDNZ NOMLY O9- OAWHX ODMLO OJQWA OK1 OVD OVEED P2P PAFKI PEELM PQQKQ Q1. Q5Y R44 RD5 RNS ROL ROX RPM RUSNO RW1 RXO SV3 TEORI TJP TLC TOX TR2 W8F WOQ X7H YAYTL YKOAZ YXANX ZKX ~91 ~KM CGR CUY CVF ECM EIF NPM 7X8 5PM ACUXJ ADGKP ADRDM ADVEK AFGWE AJEEA NU- |
| ID | FETCH-LOGICAL-c414t-b204a9af3cfee53dea1083b59eab4ceb74a054324dca4dd27a49098d3b22e90e3 |
| ISICitedReferencesCount | 911 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000871700600001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1367-4803 1367-4811 |
| IngestDate | Thu Aug 21 18:38:50 EDT 2025 Thu Oct 02 11:36:29 EDT 2025 Mon Jul 21 05:36:48 EDT 2025 Sat Nov 29 03:49:25 EST 2025 Tue Nov 18 22:11:31 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 23 |
| Language | English |
| License | https://creativecommons.org/licenses/by/4.0 The Author(s) 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c414t-b204a9af3cfee53dea1083b59eab4ceb74a054324dca4dd27a49098d3b22e90e3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ORCID | 0000-0002-9988-0866 0000-0001-6662-9010 0000-0003-0426-8445 |
| OpenAccessLink | https://pubmed.ncbi.nlm.nih.gov/PMC9710552 |
| PMID | 36218463 |
| PQID | 2723815986 |
| PQPubID | 23479 |
| PageCount | 2 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_9710552 proquest_miscellaneous_2723815986 pubmed_primary_36218463 crossref_citationtrail_10_1093_bioinformatics_btac672 crossref_primary_10_1093_bioinformatics_btac672 |
| PublicationCentury | 2000 |
| PublicationDate | 2022-11-30 |
| PublicationDateYYYYMMDD | 2022-11-30 |
| PublicationDate_xml | – month: 11 year: 2022 text: 2022-11-30 day: 30 |
| PublicationDecade | 2020 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | Bioinformatics (Oxford, England) |
| PublicationTitleAlternate | Bioinformatics |
| PublicationYear | 2022 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | Parks (2022113016193824100_btac672-B8) 2022; 50 Balaban (2022113016193824100_btac672-B2) 2022; 22 Almeida (2022113016193824100_btac672-B1) 2021; 39 Nayfach (2022113016193824100_btac672-B6) 2021; 39 Matsen (2022113016193824100_btac672-B5) 2010; 11 Parks (2022113016193824100_btac672-B7) 2020; 38 Barbera (2022113016193824100_btac672-B3) 2019; 68 Chaumeil (2022113016193824100_btac672-B4) 2019; 36 |
| References_xml | – volume: 39 start-page: 499 year: 2021 ident: 2022113016193824100_btac672-B6 article-title: A genomic catalog of earth’s microbiomes publication-title: Nat. Biotechnol doi: 10.1038/s41587-020-0718-6 – volume: 38 start-page: 1079 year: 2020 ident: 2022113016193824100_btac672-B7 article-title: A complete domain-to-species taxonomy for bacteria and archaea publication-title: Nat. Biotechnol doi: 10.1038/s41587-020-0501-8 – volume: 11 start-page: 538 year: 2010 ident: 2022113016193824100_btac672-B5 article-title: Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-538 – volume: 39 start-page: 105 year: 2021 ident: 2022113016193824100_btac672-B1 article-title: A unified catalog of 204,938 reference genomes from the human gut microbiome publication-title: Nat. Biotechnol doi: 10.1038/s41587-020-0603-3 – volume: 22 start-page: 1213 year: 2022 ident: 2022113016193824100_btac672-B2 article-title: Fast and accurate distance-based phylogenetic placement using divide and conquer publication-title: Mol. Ecol. Resour doi: 10.1111/1755-0998.13527 – volume: 68 start-page: 365 year: 2019 ident: 2022113016193824100_btac672-B3 article-title: EPA-ng: massively parallel evolutionary placement of genetic sequences publication-title: Syst. Biol doi: 10.1093/sysbio/syy054 – volume: 36 start-page: 1925 year: 2019 ident: 2022113016193824100_btac672-B4 article-title: GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz848 – volume: 50 start-page: D785 year: 2022 ident: 2022113016193824100_btac672-B8 article-title: GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy publication-title: Nucleic Acids Res doi: 10.1093/nar/gkab776 |
| SSID | ssj0005056 |
| Score | 2.7602804 |
| Snippet | The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However,... |
| SourceID | pubmedcentral proquest pubmed crossref |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | 5315 |
| SubjectTerms | Applications Note Documentation Software |
| Title | GTDB-Tk v2: memory friendly classification with the genome taxonomy database |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/36218463 https://www.proquest.com/docview/2723815986 https://pubmed.ncbi.nlm.nih.gov/PMC9710552 |
| Volume | 38 |
| WOSCitedRecordID | wos000871700600001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3db5swELfSbpP2Mu2zyz4qT5r2glASGwreW9a1m6Yo7QOdeEMGjBo1JSmlUbK_ZX_s7rCBsFVa97AXFJmALd-P853v_DtC3oNrzLLUT2w3ldx2MunY0vGVnUhYe5lI3aSKnn-feNOpH4bitNf7WZ-FWc29PPfXa7H8r6KGNhA2Hp39B3E3L4UG-A1ChyuIHa53EvyX4PMnO7iwVgy9_UvMpN1YGdIZp_ONlaC1jOlBWvB6Gxagglytl8oq5bo65WBh5mhcR27qoO9sYXhWK25nJCpd17nxphjI1sbC4bkEvae3mE9h8S2UPZ7LWd6KGAZSKZqxLGAo31qEwWBAKZc_2h2fNtJVXBjDH6u55uZshdm2AI_X0CU2mpYj4bpvNK26pc2oZ-5vwZDxLWUL6sO9dRXQDFlxZ1KwoZTJgS4U1CXenp5Ex2eTSRQchcGH5ZWNNckwdm8KtOyQe8xzBSYMBidhm0A0rGoDN4Ouz58LPuh2PTAdd02fP_yZ39Nyt-yc4DF5ZBwUOtbAekJ6Kn9KHuiSpZtnZGLgRVfsI9XgojW4aBdcFMFFAVxUg4vW4KI1uJ6Ts-Oj4PCrbSpy2Ikzcko7ZkNHCpnxJFPK5amSIzDhY1coGTuJij1HggsANnoK33qaMk86Yij8lMeMKTFU_AXZzRe5ekkoEwwpTcE_l-Ckg37IwJbm0otdjyk-dPrErScrSgxdPVZNmUc6bYJH3UmOzCT3yaB5bqkJW_76xLtaFhHoVgyYyVwtbq4jhhX5RljBoE_2tGyad4LhNwLbnfeJ15Fa8wfkbe_eyWfnFX-78LAqLXt1h35fk4ftx_OG7JbFjXpL7iercnZd7JMdL_T3K1T-AjjIwPM |
| linkProvider | Oxford University Press |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=GTDB-Tk+v2%3A+memory+friendly+classification+with+the+genome+taxonomy+database&rft.jtitle=Bioinformatics+%28Oxford%2C+England%29&rft.au=Chaumeil%2C+Pierre-Alain&rft.au=Mussig%2C+Aaron+J&rft.au=Hugenholtz%2C+Philip&rft.au=Parks%2C+Donovan+H&rft.date=2022-11-30&rft.issn=1367-4811&rft.eissn=1367-4811&rft.volume=38&rft.issue=23&rft.spage=5315&rft_id=info:doi/10.1093%2Fbioinformatics%2Fbtac672&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1367-4803&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1367-4803&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1367-4803&client=summon |