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chore: update data catalog 2025-06-22
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‎catalog/build/intermediate/genomes-from-ncbi.tsv

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@@ -697,7 +697,7 @@ IHEM 14462 563466 GCF_000732125.1 True Scaffold 43437139 176 1380919 11 280 50.
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ERTm6 1913371 GCF_000738915.1 True Scaffold 4276041 24 797226 3 118 38.5 Full annotation GCA_000738915.1 Nematocida ausubeli 1913371 1,131567,2759,33154,4751,112252,6029,469895,586132,1913371 Microsporidia Eukaryota Fungi Microsporidia Nematocida Nematocida ausubeli 2759 4751 6029 586132 1913371 https://genome.ucsc.edu/h/GCF_000738915.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/738/915/GCF_000738915.1/genes/GCF_000738915.1_Nema_sp_1_ERTm6_V2.ncbiRefSeq.gtf.gz
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Shintoku 869250 GCF_000740895.1 True Chromosome 4.0 8983596 4 2216979 2 41.5 GCA_000740895.1 Theileria orientalis 68886 1,131567,2759,2698737,33630,5794,422676,5863,27994,5873,68886,869250 Apicomplexa Eukaryota Apicomplexa Aconoidasida Piroplasmida Theileriidae Theileria Theileria orientalis Theileria orientalis strain Shintoku 2759 5794 422676 5863 27994 5873 68886 869250 https://genome.ucsc.edu/h/GCF_000740895.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/740/895/GCF_000740895.1/genes/GCF_000740895.1_ASM74089v1.ncbiRefSeq.gtf.gz
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AT-1 334545 GCF_000751075.1 True Contig 1453216 27 132848 4 140 32.5 GCA_000751075.1 Rickettsia tamurae 334545 1,131567,2,3379134,1224,28211,766,775,33988,780,114277,334545 Bacteria Bacteria Pseudomonadati Pseudomonadota Alphaproteobacteria Rickettsiales Rickettsiaceae Rickettsia Rickettsia tamurae 2 3379134 1224 28211 766 775 780 334545 https://genome.ucsc.edu/h/GCF_000751075.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/751/075/GCF_000751075.1/genes/GCF_000751075.1_Rickettsia_tamurae_AT-1.ncbiGene.gtf.gz
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MHOM/PA/94/PSC-1 5679 GCF_000755165.1 True Chromosome 35.0 30688794 35 1043456 10 30 57.5 GCA_000755165.1 Leishmania panamensis 5679 1,131567,2759,2611352,33682,5653,2704647,2704949,5654,1286322,5658,37616,38579,5679 Kinetoplastea Eukaryota Euglenozoa Kinetoplastea Trypanosomatida Trypanosomatidae Leishmania Leishmania panamensis 2759 33682 5653 2704949 5654 5658 5679 https://genome.ucsc.edu/h/GCF_000755165.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/755/165/GCF_000755165.1/genes/GCF_000755165.1_ASM75516v1.ncbiRefSeq.gtf.gz
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MHOM/PA/94/PSC-1 5679 GCF_000755165.1 True Chromosome 35.0 30688794 35 1043456 10 100 57.5 GCA_000755165.1 Leishmania panamensis 5679 1,131567,2759,2611352,33682,5653,2704647,2704949,5654,1286322,5658,37616,38579,5679 Kinetoplastea Eukaryota Euglenozoa Kinetoplastea Trypanosomatida Trypanosomatidae Leishmania Leishmania panamensis 2759 33682 5653 2704949 5654 5658 5679 https://genome.ucsc.edu/h/GCF_000755165.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/755/165/GCF_000755165.1/genes/GCF_000755165.1_ASM75516v1.ncbiRefSeq.gtf.gz
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UGP3 1485682 GCF_000760515.2 True Contig 5635072 610 32179 50 300 43.0 Full annotation GCA_000760515.2 Mitosporidium daphniae 1485682 1,131567,2759,33154,4751,112252,6029,469895,1633384,1485682 Microsporidia Eukaryota Fungi Microsporidia Mitosporidium Mitosporidium daphniae 2759 4751 6029 1633384 1485682 https://genome.ucsc.edu/h/GCF_000760515.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/760/515/GCF_000760515.2/genes/GCF_000760515.2_UGP1.1.ncbiRefSeq.gtf.gz
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CHN_HEN01 88456 GCF_000769155.1 False Scaffold 44034411 2297 61202 217 Full annotation GCA_000769155.2 Cyclospora cayetanensis 88456 1,131567,2759,2698737,33630,5794,1280412,5796,75739,423054,5799,44417,88456 Apicomplexa Eukaryota Apicomplexa Conoidasida Eucoccidiorida Eimeriidae Cyclospora Cyclospora cayetanensis 2759 5794 1280412 75739 5799 44417 88456 https://genome.ucsc.edu/h/GCF_000769155.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/769/155/GCF_000769155.1/genes/GCF_000769155.1_ASM76915v2.ncbiRefSeq.gtf.gz
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OC4 1354746 GCF_000803265.1 True Contig 2290528 15 228601 5 627 38.5 Full annotation GCA_000803265.1 Ordospora colligata 174685 1,131567,2759,33154,4751,112252,6029,469895,174683,174684,174685,1354746 Microsporidia Eukaryota Fungi Microsporidia Ordosporidae Ordospora Ordospora colligata Ordospora colligata OC4 2759 4751 6029 174683 174684 174685 1354746 https://genome.ucsc.edu/h/GCF_000803265.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/803/265/GCF_000803265.1/genes/GCF_000803265.1_ASM80326v1.ncbiRefSeq.gtf.gz

‎catalog/build/intermediate/outbreak-taxonomy-mapping.tsv

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taxonomy_id name rank
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5052 Aspergillus GENUS
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38574 Leishmania donovani species complex SPECIES_GROUP
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1980418 Phenuiviridae FAMILY
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12058 Picornaviridae FAMILY
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199306 Coccidioides posadasii SPECIES
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11617 Arenaviridae FAMILY
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3418604 Betacoronavirus pandemicum SPECIES
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5037 Histoplasma capsulatum SPECIES
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1980415 Nairoviridae FAMILY
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4827 Mucorales ORDER
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1980416 Peribunyaviridae FAMILY
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1980413 Hantaviridae FAMILY
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1773 Mycobacterium tuberculosis SPECIES
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11158 Paramyxoviridae FAMILY
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4827 Mucorales ORDER
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11050 Flaviviridae FAMILY
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11018 Togaviridae FAMILY
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498019 Candidozyma auris SPECIES
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5763 Naegleria fowleri SPECIES
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5207 Cryptococcus neoformans SPECIES
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11158 Paramyxoviridae FAMILY
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5833 Plasmodium falciparum SPECIES
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5037 Histoplasma capsulatum SPECIES
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1773 Mycobacterium tuberculosis SPECIES
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5052 Aspergillus GENUS
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1980415 Nairoviridae FAMILY
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12058 Picornaviridae FAMILY
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1980416 Peribunyaviridae FAMILY
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498019 Candidozyma auris SPECIES
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5807 Cryptosporidium parvum SPECIES
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11266 Filoviridae FAMILY
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10244 Monkeypox virus
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3418604 Betacoronavirus pandemicum SPECIES
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11320 Influenza A virus
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199306 Coccidioides posadasii SPECIES
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10244 Monkeypox virus
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5763 Naegleria fowleri SPECIES
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11617 Arenaviridae FAMILY
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11266 Filoviridae FAMILY

‎catalog/output/qc-report.md

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- Alphapapillomavirus 12: 990303, 10570
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- Alphapapillomavirus 14: 120686, 333769
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- Alphapapillomavirus 6: 333765, 10611
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- Asfivirus haemorrhagiae: 443876, 10497, 443878
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- Betacoronavirus pandemicum: 2697049, 227984
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- Betapapillomavirus 1: 889813, 333923
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- Blumeria graminis: 62690, 1689686
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- Brisavirus: 3116878, 2571078, 2571075, 2571077
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- Asfivirus haemorrhagiae: 443878, 443876, 10497
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- Betacoronavirus pandemicum: 227984, 2697049
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- Betapapillomavirus 1: 333923, 889813
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- Blumeria graminis: 1689686, 62690
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- Brisavirus: 3116878, 2571077, 2571078, 2571075
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- Candida tropicalis strain MYA-3404: 5482, 294747
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- Cryptococcus neoformans strain H99: 235443, 5207
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- Cryptococcus neoformans strain H99: 5207, 235443
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- Cryptosporidium parvum: 353152, 5807
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- Deltaretrovirus priTlym1: 11908, 194440
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- Deltaretrovirus priTlym1: 194440, 11908
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- Dependoparvovirus mammalian1: 82300, 256548
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- Dependoparvovirus primate1: 202812, 85106, 57579, 202813, 10804
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- Enterovirus A: 156647, 150846
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- Dependoparvovirus primate1: 10804, 85106, 202813, 202812, 57579
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- Enterovirus A: 150846, 156647
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- Gammapapillomavirus 11: 1070409, 1195796, 1070413
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- Gammapapillomavirus 12: 909331, 746832
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- Gammapapillomavirus 15: 1070408, 1472342
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- Gammapapillomavirus 15: 1472342, 1070408
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- Gammapapillomavirus 19: 1315259, 1315264
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- Gemykibivirus humas1: 1519409, 1516081
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- Glossina fuscipes: 7396, 201502
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- Hepacivirus hominis: 1544901, 33745, 356114
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- Neospora caninum strain Liverpool: 572307, 29176
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- Norovirus norwalkense: 490039, 1246677, 122928, 1529918, 1529924, 1529909, 122929
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- Orthoflavivirus denguei: 11069, 11070, 11053
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- Orthomarburgvirus marburgense: 448086, 3052505
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- Neospora caninum strain Liverpool: 29176, 572307
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- Norovirus norwalkense: 1246677, 490039, 1529924, 122928, 122929, 1529918, 1529909
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- Orthoflavivirus denguei: 11070, 11069, 11053
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- Orthomarburgvirus marburgense: 3052505, 448086
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- Pegivirus columbiaense: 1729141, 1704090
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- Plasmodium falciparum: 5833, 36329
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- Plasmodium vinckei: 119398, 138297, 138298, 54757, 5860
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- Rhinovirus B: 12131, 44130
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- Plasmodium vinckei: 5860, 138298, 119398, 54757, 138297
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- Rhinovirus B: 44130, 12131
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- Small anellovirus: 289366, 289367
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- Trypanosoma brucei: 5702, 185431
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- Trypanosoma cruzi strain Dm28c: 5693, 1416333, 85057
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- Vesivirus exanthema: 35612, 146073
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- Trypanosoma cruzi strain Dm28c: 5693, 85057, 1416333
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- Vesivirus exanthema: 146073, 35612
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## Assemblies without ploidy information
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