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chore: update data catalog 2025-06-22 #551

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2 changes: 1 addition & 1 deletion catalog/build/intermediate/genomes-from-ncbi.tsv
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Expand Up @@ -697,7 +697,7 @@ IHEM 14462 563466 GCF_000732125.1 True Scaffold 43437139 176 1380919 11 280 50.
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
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
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
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
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
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
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
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
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30 changes: 15 additions & 15 deletions catalog/build/intermediate/outbreak-taxonomy-mapping.tsv
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@@ -1,25 +1,25 @@
taxonomy_id name rank
5052 Aspergillus GENUS
38574 Leishmania donovani species complex SPECIES_GROUP
1980418 Phenuiviridae FAMILY
12058 Picornaviridae FAMILY
199306 Coccidioides posadasii SPECIES
11617 Arenaviridae FAMILY
3418604 Betacoronavirus pandemicum SPECIES
5037 Histoplasma capsulatum SPECIES
1980415 Nairoviridae FAMILY
4827 Mucorales ORDER
1980416 Peribunyaviridae FAMILY
1980413 Hantaviridae FAMILY
1773 Mycobacterium tuberculosis SPECIES
11158 Paramyxoviridae FAMILY
4827 Mucorales ORDER
11050 Flaviviridae FAMILY
11018 Togaviridae FAMILY
498019 Candidozyma auris SPECIES
5763 Naegleria fowleri SPECIES
5207 Cryptococcus neoformans SPECIES
11158 Paramyxoviridae FAMILY
5833 Plasmodium falciparum SPECIES
5037 Histoplasma capsulatum SPECIES
1773 Mycobacterium tuberculosis SPECIES
5052 Aspergillus GENUS
1980415 Nairoviridae FAMILY
12058 Picornaviridae FAMILY
1980416 Peribunyaviridae FAMILY
498019 Candidozyma auris SPECIES
5807 Cryptosporidium parvum SPECIES
11266 Filoviridae FAMILY
10244 Monkeypox virus
3418604 Betacoronavirus pandemicum SPECIES
11320 Influenza A virus
199306 Coccidioides posadasii SPECIES
10244 Monkeypox virus
5763 Naegleria fowleri SPECIES
11617 Arenaviridae FAMILY
11266 Filoviridae FAMILY
36 changes: 18 additions & 18 deletions catalog/output/qc-report.md
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Expand Up @@ -27,37 +27,37 @@ None
- Alphapapillomavirus 12: 990303, 10570
- Alphapapillomavirus 14: 120686, 333769
- Alphapapillomavirus 6: 333765, 10611
- Asfivirus haemorrhagiae: 443876, 10497, 443878
- Betacoronavirus pandemicum: 2697049, 227984
- Betapapillomavirus 1: 889813, 333923
- Blumeria graminis: 62690, 1689686
- Brisavirus: 3116878, 2571078, 2571075, 2571077
- Asfivirus haemorrhagiae: 443878, 443876, 10497
- Betacoronavirus pandemicum: 227984, 2697049
- Betapapillomavirus 1: 333923, 889813
- Blumeria graminis: 1689686, 62690
- Brisavirus: 3116878, 2571077, 2571078, 2571075
- Candida tropicalis strain MYA-3404: 5482, 294747
- Cryptococcus neoformans strain H99: 235443, 5207
- Cryptococcus neoformans strain H99: 5207, 235443
- Cryptosporidium parvum: 353152, 5807
- Deltaretrovirus priTlym1: 11908, 194440
- Deltaretrovirus priTlym1: 194440, 11908
- Dependoparvovirus mammalian1: 82300, 256548
- Dependoparvovirus primate1: 202812, 85106, 57579, 202813, 10804
- Enterovirus A: 156647, 150846
- Dependoparvovirus primate1: 10804, 85106, 202813, 202812, 57579
- Enterovirus A: 150846, 156647
- Gammapapillomavirus 11: 1070409, 1195796, 1070413
- Gammapapillomavirus 12: 909331, 746832
- Gammapapillomavirus 15: 1070408, 1472342
- Gammapapillomavirus 15: 1472342, 1070408
- Gammapapillomavirus 19: 1315259, 1315264
- Gemykibivirus humas1: 1519409, 1516081
- Glossina fuscipes: 7396, 201502
- Hepacivirus hominis: 1544901, 33745, 356114
- Neospora caninum strain Liverpool: 572307, 29176
- Norovirus norwalkense: 490039, 1246677, 122928, 1529918, 1529924, 1529909, 122929
- Orthoflavivirus denguei: 11069, 11070, 11053
- Orthomarburgvirus marburgense: 448086, 3052505
- Neospora caninum strain Liverpool: 29176, 572307
- Norovirus norwalkense: 1246677, 490039, 1529924, 122928, 122929, 1529918, 1529909
- Orthoflavivirus denguei: 11070, 11069, 11053
- Orthomarburgvirus marburgense: 3052505, 448086
- Pegivirus columbiaense: 1729141, 1704090
- Plasmodium falciparum: 5833, 36329
- Plasmodium vinckei: 119398, 138297, 138298, 54757, 5860
- Rhinovirus B: 12131, 44130
- Plasmodium vinckei: 5860, 138298, 119398, 54757, 138297
- Rhinovirus B: 44130, 12131
- Small anellovirus: 289366, 289367
- Trypanosoma brucei: 5702, 185431
- Trypanosoma cruzi strain Dm28c: 5693, 1416333, 85057
- Vesivirus exanthema: 35612, 146073
- Trypanosoma cruzi strain Dm28c: 5693, 85057, 1416333
- Vesivirus exanthema: 146073, 35612

## Assemblies without ploidy information

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