From ed64933d4c9ab632d77d2d569af84d639aa89842 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Sat, 21 Sep 2024 21:15:07 -0700 Subject: [PATCH 1/2] chore: update organisms list for 2024-09-20 (#89) --- files/build-genomes-files.py | 2 +- files/out/genomes.json | 539 +++++++++++++++++++++++++++++++++++ files/source/genomes.tsv | 49 ++++ 3 files changed, 589 insertions(+), 1 deletion(-) diff --git a/files/build-genomes-files.py b/files/build-genomes-files.py index 2736a59..dabb1f8 100644 --- a/files/build-genomes-files.py +++ b/files/build-genomes-files.py @@ -3,7 +3,7 @@ import requests GENOMES_SOURCE_URL = "https://docs.google.com/spreadsheets/d/1NRfTvebPl6zJ0l9tCqBtq6YCrwV6_XDBlheq3L5HcvQ/gviz/tq?tqx=out:csv&sheet=GenomeDataTypes_Summary.csv" -ASSEMBLIES_URL = "https://hgdownload.soe.ucsc.edu/hubs/BRC/assembly.list.json" +ASSEMBLIES_URL = "https://hgdownload.soe.ucsc.edu/hubs/BRC/assemblyList.json" OUTPUT_PATH = "files/source/genomes.tsv" diff --git a/files/out/genomes.json b/files/out/genomes.json index af611e4..878a2f4 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -219,6 +219,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003835.1", "vEuPathDbProject": "FungiDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000003855.2", + "organism": "Blastomyces gilchristii SLH14081", + "species": "Blastomyces gilchristii", + "strain": "SLH14081", + "supercontigs": 100, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003855.2", + "vEuPathDbProject": "FungiDB" + }, { "chromosomes": 0, "contigs": 0, @@ -274,6 +285,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006355.2", "vEuPathDbProject": "PlasmoDB" }, + { + "chromosomes": 0, + "contigs": 1422, + "genomeVersionAssemblyId": "GCA_000006425.1", + "organism": "Cryptosporidium hominis TU502", + "species": "Cryptosporidium hominis", + "strain": "TU502", + "supercontigs": 0, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006425.1", + "vEuPathDbProject": "CryptoDB" + }, { "chromosomes": 7, "contigs": 0, @@ -538,6 +560,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149685.1", "vEuPathDbProject": "FungiDB" }, + { + "chromosomes": 14, + "contigs": 2034, + "genomeVersionAssemblyId": "GCA_000149715.2", + "organism": "Toxoplasma gondii GT1", + "species": "Toxoplasma gondii", + "strain": "GT1", + "supercontigs": 0, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149715.2", + "vEuPathDbProject": "ToxoDB" + }, { "chromosomes": 0, "contigs": 0, @@ -571,6 +604,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149845.2", "vEuPathDbProject": "FungiDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000149865.1", + "organism": "Batrachochytrium dendrobatidis JEL423", + "species": "Batrachochytrium dendrobatidis", + "strain": "JEL423", + "supercontigs": 69, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149865.1", + "vEuPathDbProject": "FungiDB" + }, { "chromosomes": 0, "contigs": 0, @@ -824,6 +868,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000151175.1", "vEuPathDbProject": "FungiDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000151295.1", + "organism": "Allomyces macrogynus ATCC 38327", + "species": "Allomyces macrogynus", + "strain": "ATCC 38327", + "supercontigs": 101, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000151295.1", + "vEuPathDbProject": "FungiDB" + }, { "chromosomes": 0, "contigs": 0, @@ -1319,6 +1374,72 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000223845.1", "vEuPathDbProject": "CryptoDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000224805.2", + "organism": "Toxoplasma gondii RUB", + "species": "Toxoplasma gondii", + "strain": "RUB", + "supercontigs": 2424, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224805.2", + "vEuPathDbProject": "ToxoDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000224825.2", + "organism": "Toxoplasma gondii TgCATBr9", + "species": "Toxoplasma gondii", + "strain": "TgCATBr9", + "supercontigs": 2452, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224825.2", + "vEuPathDbProject": "ToxoDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000224845.2", + "organism": "Toxoplasma gondii VAND", + "species": "Toxoplasma gondii", + "strain": "VAND", + "supercontigs": 2137, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224845.2", + "vEuPathDbProject": "ToxoDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000224865.2", + "organism": "Toxoplasma gondii MAS", + "species": "Toxoplasma gondii", + "strain": "MAS", + "supercontigs": 2180, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224865.2", + "vEuPathDbProject": "ToxoDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000224885.2", + "organism": "Toxoplasma gondii p89", + "species": "Toxoplasma gondii", + "strain": "p89", + "supercontigs": 2150, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224885.2", + "vEuPathDbProject": "ToxoDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000224905.2", + "organism": "Toxoplasma gondii FOU", + "species": "Toxoplasma gondii", + "strain": "FOU", + "supercontigs": 2869, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224905.2", + "vEuPathDbProject": "ToxoDB" + }, { "chromosomes": 0, "contigs": 3076, @@ -1528,6 +1649,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000250755.2", "vEuPathDbProject": "TriTrypDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000250965.2", + "organism": "Toxoplasma gondii ARI", + "species": "Toxoplasma gondii", + "strain": "ARI", + "supercontigs": 2723, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000250965.2", + "vEuPathDbProject": "ToxoDB" + }, { "chromosomes": 0, "contigs": 0, @@ -1913,6 +2045,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000338675.2", "vEuPathDbProject": "ToxoDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000338855.1", + "organism": "Entamoeba histolytica KU27", + "species": "Entamoeba histolytica", + "strain": "KU27", + "supercontigs": 1796, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000338855.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -1957,6 +2100,28 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000342415.1", "vEuPathDbProject": "PiroplasmaDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000344925.1", + "organism": "Entamoeba histolytica HM-1:IMSS-B", + "species": "Entamoeba histolytica", + "strain": "HM-1:IMSS-B", + "supercontigs": 1938, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000344925.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000346345.1", + "organism": "Entamoeba histolytica HM-3:IMSS", + "species": "Entamoeba histolytica", + "strain": "HM-3:IMSS", + "supercontigs": 1880, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000346345.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -2122,6 +2287,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000365225.1", "vEuPathDbProject": "TriTrypDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000365475.1", + "organism": "Entamoeba histolytica HM-1:IMSS-A", + "species": "Entamoeba histolytica", + "strain": "HM-1:IMSS-A", + "supercontigs": 1685, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000365475.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -2881,6 +3057,149 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000820605.1", "vEuPathDbProject": "FungiDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826245.1", + "organism": "Acanthamoeba astronyxis Unknown", + "species": "Acanthamoeba astronyxis", + "strain": "Unknown", + "supercontigs": 98248, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826245.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826265.1", + "organism": "Acanthamoeba culbertsoni A1", + "species": "Acanthamoeba culbertsoni", + "strain": "A1", + "supercontigs": 72411, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826265.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826285.1", + "organism": "Acanthamoeba lenticulata PD2S", + "species": "Acanthamoeba lenticulata", + "strain": "PD2S", + "supercontigs": 79048, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826285.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826305.1", + "organism": "Acanthamoeba palestinensis Reich", + "species": "Acanthamoeba palestinensis", + "strain": "Reich", + "supercontigs": 26188, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826305.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826325.1", + "organism": "Acanthamoeba triangularis SH621", + "species": "Acanthamoeba triangularis", + "strain": "SH621", + "supercontigs": 56742, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826325.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826345.1", + "organism": "Acanthamoeba sp T4b-type", + "species": "Acanthamoeba sp.", + "strain": "T4B-type", + "supercontigs": 224482, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826345.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826365.1", + "organism": "Acanthamoeba sp Incertae sedis", + "species": "Acanthamoeba sp.", + "strain": "Incertae_sedis", + "supercontigs": 24098, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826365.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826385.1", + "organism": "Acanthamoeba rhysodes Singh", + "species": "Acanthamoeba rhysodes", + "strain": "Singh", + "supercontigs": 62836, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826385.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826425.1", + "organism": "Acanthamoeba lugdunensis L3a", + "species": "Acanthamoeba lugdunensis", + "strain": "L3a", + "supercontigs": 67459, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826425.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826445.1", + "organism": "Acanthamoeba quina Vil3", + "species": "Acanthamoeba quina", + "strain": "Vil3", + "supercontigs": 60490, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826445.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826465.1", + "organism": "Acanthamoeba mauritaniensis 1652", + "species": "Acanthamoeba mauritaniensis", + "strain": "1652", + "supercontigs": 67233, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826465.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826485.1", + "organism": "Acanthamoeba castellanii Ma", + "species": "Acanthamoeba castellanii", + "strain": "Ma", + "supercontigs": 221748, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826485.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_000826505.1", + "organism": "Acanthamoeba sp Galka", + "species": "Acanthamoeba sp.", + "strain": "Galka", + "supercontigs": 224137, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826505.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -3167,6 +3486,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001179505.1", "vEuPathDbProject": "CryptoDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_001185145.1", + "organism": "Balamuthia mandrillaris CDC-V039", + "species": "Balamuthia mandrillaris", + "strain": "CDC-V039", + "supercontigs": 1604, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001185145.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -3178,6 +3508,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001189475.1", "vEuPathDbProject": "FungiDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_001262475.1", + "organism": "Balamuthia mandrillaris strain 2046", + "species": "Balamuthia mandrillaris", + "strain": "strain 2046", + "supercontigs": 14699, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001262475.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -4036,6 +4377,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002219105.2", "vEuPathDbProject": "TriTrypDB" }, + { + "chromosomes": 13, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_002219185.1", + "organism": "Nakaseomyces glabratus DSY562", + "species": "Nakaseomyces glabratus", + "strain": "DSY562", + "supercontigs": 5, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002219185.1", + "vEuPathDbProject": "FungiDB" + }, { "chromosomes": 8, "contigs": 0, @@ -4223,6 +4575,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002897235.1", "vEuPathDbProject": "PiroplasmaDB" }, + { + "chromosomes": 0, + "contigs": 3460, + "genomeVersionAssemblyId": "GCA_002914575.1", + "organism": "Entamoeba moshkovskii Laredo", + "species": "Entamoeba moshkovskii", + "strain": "Laredo", + "supercontigs": 1147, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002914575.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -4850,6 +5213,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004325075.1", "vEuPathDbProject": "MicrosporidiaDB" }, + { + "chromosomes": 5, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_004337985.1", + "organism": "Pyricularia pennisetigena Br36", + "species": "Pyricularia pennisetigena", + "strain": "Br36", + "supercontigs": 103, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_004337985.1", + "vEuPathDbProject": "FungiDB" + }, { "chromosomes": 0, "contigs": 0, @@ -5169,6 +5543,28 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013177555.1", "vEuPathDbProject": "FungiDB" }, + { + "chromosomes": 11, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_013339685.2", + "organism": "Hyalomma asiaticum Hyas-2018", + "species": "Hyalomma asiaticum", + "strain": "Hyas-2018", + "supercontigs": 6308, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013339685.2", + "vEuPathDbProject": "VectorBase" + }, + { + "chromosomes": 11, + "contigs": 7036, + "genomeVersionAssemblyId": "GCA_013339725.1", + "organism": "Rhipicephalus microplus Rmic-2018", + "species": "Rhipicephalus microplus", + "strain": "Rmic-2018", + "supercontigs": 0, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_013339725.1", + "vEuPathDbProject": "VectorBase" + }, { "chromosomes": 11, "contigs": 0, @@ -5180,6 +5576,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_013339745.2", "vEuPathDbProject": "VectorBase" }, + { + "chromosomes": 11, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_013339765.2", + "organism": "Haemaphysalis longicornis HaeL-2018", + "species": "Haemaphysalis longicornis", + "strain": "HaeL-2018", + "supercontigs": 3874, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013339765.2", + "vEuPathDbProject": "VectorBase" + }, { "chromosomes": 0, "contigs": 0, @@ -5191,6 +5598,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013358655.1", "vEuPathDbProject": "TriTrypDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_013358835.2", + "organism": "Ixodes persulcatus Iper-2018", + "species": "Ixodes persulcatus", + "strain": "Iper-2018", + "supercontigs": 11596, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013358835.2", + "vEuPathDbProject": "VectorBase" + }, { "chromosomes": 0, "contigs": 0, @@ -5345,6 +5763,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_015227675.2", "vEuPathDbProject": "HostDB" }, + { + "chromosomes": 8, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_015245375.1", + "organism": "Cryptosporidium parvum IOWA-ATCC", + "species": "Cryptosporidium parvum", + "strain": "IOWA-ATCC", + "supercontigs": 0, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_015245375.1", + "vEuPathDbProject": "CryptoDB" + }, { "chromosomes": 3, "contigs": 53, @@ -5642,6 +6071,28 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018398765.1", "vEuPathDbProject": "CryptoDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_018466815.1", + "organism": "Entamoeba histolytica DS4-868", + "species": "Entamoeba histolytica", + "strain": "DS4-868", + "supercontigs": 1177, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018466815.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_019059535.1", + "organism": "Entamoeba histolytica KU48", + "species": "Entamoeba histolytica", + "strain": "KU48", + "supercontigs": 1168, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_019059535.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 11, "contigs": 685, @@ -5675,6 +6126,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_019968955.1", "vEuPathDbProject": "CryptoDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_020283535.1", + "organism": "Entamoeba histolytica KU50", + "species": "Entamoeba histolytica", + "strain": "KU50", + "supercontigs": 1063, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020283535.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -5741,6 +6203,28 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020844765.3", "vEuPathDbProject": "PlasmoDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_021020595.1", + "organism": "Acanthamoeba castellanii C3", + "species": "Acanthamoeba castellanii", + "strain": "C3", + "supercontigs": 174, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_021020595.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_021020605.1", + "organism": "Acanthamoeba castellanii str. Neff 2021", + "species": "Acanthamoeba castellanii", + "strain": "str. Neff 2021", + "supercontigs": 111, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_021020605.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -5917,6 +6401,39 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_026262505.1", "vEuPathDbProject": "TrichDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_027943245.1", + "organism": "Acanthamoeba sp. SK_2022b", + "species": "Acanthamoeba sp.", + "strain": "SK_2022b", + "supercontigs": 1790, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_027943245.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_027943295.1", + "organism": "Acanthamoeba sp. SK_2022a", + "species": "Acanthamoeba sp.", + "strain": "SK_2022a", + "supercontigs": 2108, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_027943295.1", + "vEuPathDbProject": "AmoebaDB" + }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_027944975.1", + "organism": "Acanthamoeba sp. SK_2022c", + "species": "Acanthamoeba sp.", + "strain": "SK_2022c", + "supercontigs": 20778, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_027944975.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 0, "contigs": 0, @@ -6500,6 +7017,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_902459845.2", "vEuPathDbProject": "PlasmoDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_902651635.1", + "organism": "Mastigamoeba balamuthi ATCC 30984", + "species": "Mastigamoeba balamuthi", + "strain": "ATCC 30984", + "supercontigs": 1925, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_902651635.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 14, "contigs": 0, @@ -6599,6 +7127,17 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_916722125.1", "vEuPathDbProject": "TriTrypDB" }, + { + "chromosomes": 0, + "contigs": 0, + "genomeVersionAssemblyId": "GCA_917563895.1", + "organism": "Entamoeba histolytica Rahman", + "species": "Entamoeba histolytica", + "strain": "Rahman", + "supercontigs": 18523, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_917563895.1", + "vEuPathDbProject": "AmoebaDB" + }, { "chromosomes": 13, "contigs": 0, diff --git a/files/source/genomes.tsv b/files/source/genomes.tsv index a1d4bd2..3e51dd8 100644 --- a/files/source/genomes.tsv +++ b/files/source/genomes.tsv @@ -11,6 +11,7 @@ Trypanosoma congolense IL3000 GenBank GCA_000227395.2 yes 2828 0 11 Trypanosoma Pneumocystis murina B123 INSDC GCA_000349005.2 yes 0 20 0 Pneumocystis murina B123 FungiDB 1069680.0 GCF_000349005.2_Pneumo_murina_B123_V4 GCA_000349005.2 GCF_000349005.2 True Pneumocystis murina B123 ascomycetes P.murina B123 https://genome.ucsc.edu/h/GCF_000349005.2 Aspergillus wentii DTO 134E9 GenBank GCA_001890725.1 yes 0 27 0 Aspergillus wentii DTO 134E9 FungiDB 1073089.0 GCF_001890725.1_Aspwe1 GCA_001890725.1 GCF_001890725.1 True Aspergillus wentii DTO 134E9 ascomycetes A.wentii DTO 134E9 https://genome.ucsc.edu/h/GCF_001890725.1 Penicilliopsis zonata CBS 506.65 GenBank GCA_001890105.1 yes 0 246 0 Penicilliopsis zonata CBS 506.65 FungiDB 1073090.0 GCF_001890105.1_Aspzo1 GCA_001890105.1 GCF_001890105.1 True Penicilliopsis zonata CBS 506.65 ascomycetes P.zonata CBS 506.65 https://genome.ucsc.edu/h/GCF_001890105.1 +Toxoplasma gondii ARI GenBank GCA_000250965.2 no 0 2723 0 Toxoplasma gondii ARI ToxoDB 1074872.0 GCA_000250965.2_TGARI_v2 GCA_000250965.2 False Toxoplasma gondii ARI apicomplexans T.gondii (ARI 2016) https://genome.ucsc.edu/h/GCA_000250965.2 Toxoplasma gondii COUG GenBank GCA_000338675.2 no 4075 105 0 Toxoplasma gondii COUG ToxoDB 1074873.0 GCA_000338675.2_TGCOUG_v2 GCA_000338675.2 False Toxoplasma gondii COUG apicomplexans T.gondii (COUG 2017) https://genome.ucsc.edu/h/GCA_000338675.2 Pyronema omphalodes CBS 100304 INSDC GCA_024516155.1 yes 0 260 0 Pyronema omphalodes CBS 100304 FungiDB 337075.0 GCA_024516155.1_Pyrom1 GCA_024516155.1 False Pyronema omphalodes ascomycetes P.omphalodes (CBS 144459 2022) https://genome.ucsc.edu/h/GCA_024516155.1 Fusarium odoratissimum NRRL 54006 GenBank GCA_000260195.2 no 0 418 0 Fusarium odoratissimum NRRL 54006 FungiDB 1089451.0 GCF_000260195.1_FO_II5_V1 GCA_000260195.2 GCF_000260195.1 True Fusarium odoratissimum NRRL 54006 ascomycetes F.odoratissimum NRRL 54006 https://genome.ucsc.edu/h/GCF_000260195.1 @@ -71,6 +72,7 @@ Cryptococcus gattii EJB2 GenBank GCA_000835745.1 no 0 282 0 Cryptococcus gattii Cryptococcus gattii NT-10 GenBank GCA_000935105.1 no 0 226 0 Cryptococcus gattii VGI NT10 FungiDB 1296108.0 GCA_000935105.1_Cryp_gatt_NT-10_V1 GCA_000935105.1 False Cryptococcus gattii NT-10 basidiomycetes C.gattii (NT-10 2015) https://genome.ucsc.edu/h/GCA_000935105.1 Cryptococcus gattii CA1873 GenBank GCA_000855695.1 no 0 33 0 Cryptococcus gattii VGIII CA1873 FungiDB 1296111.0 GCA_000855695.1_Cryp_gatt_CA1873_V1 GCA_000855695.1 False Cryptococcus bacillisporus CA1873 basidiomycetes C.bacillisporus (CA1873 2015) https://genome.ucsc.edu/h/GCA_000855695.1 Kwoniella heveanensis CBS 569 GenBank GCA_000507425.3 yes 0 242 0 Kwoniella heveanensis CBS 569 FungiDB 1296119.0 GCA_000507425.3_Cryp_heve_CBS569_V2 GCA_000507425.3 False Kwoniella heveanensis CBS 569 basidiomycetes K.heveanensis (CBS 569 2016) https://genome.ucsc.edu/h/GCA_000507425.3 +Mastigamoeba balamuthi ATCC 30984 INSDC GCA_902651635.1 yes 0 1925 0 Mastigamoeba balamuthi ATCC 30984 AmoebaDB 108607.0 GCA_902651635.1_mastiga_genome_v5.1 GCA_902651635.1 False Mastigamoeba balamuthi M.balamuthi (2019) https://genome.ucsc.edu/h/GCA_902651635.1 Lentinus tigrinus ALCF2SS1-7 INSDC GCA_003813185.1 yes 0 207 0 Lentinus tigrinus ALCF2SS1-7 FungiDB 1328758.0 GCA_003813185.1_Lenti7_1 GCA_003813185.1 False Lentinus tigrinus ALCF2SS1-7 basidiomycetes L.tigrinus (ALCF2SS1-7 2018) https://genome.ucsc.edu/h/GCA_003813185.1 Aspergillus niger ATCC 13496 GenBank GCA_003344705.1 no 0 133 0 Aspergillus niger ATCC 13496 FungiDB 1353008.0 GCA_003344705.1_Aspni_bvT_1 GCA_003344705.1 False Aspergillus niger ATCC 13496 ascomycetes A.niger (ATCC 13496 2018) https://genome.ucsc.edu/h/GCA_003344705.1 Ordospora colligata OC4 GenBank GCA_000803265.1 yes 15 0 0 Ordospora colligata OC4 MicrosporidiaDB 1354746.0 GCF_000803265.1_ASM80326v1 GCA_000803265.1 GCF_000803265.1 True Ordospora colligata OC4 microsporidians O.colligata OC4 https://genome.ucsc.edu/h/GCF_000803265.1 @@ -126,6 +128,9 @@ Debaryomyces hansenii CBS767 INSDC GCA_000006445.2 yes 0 0 7 Debaryomyces hansen Nakaseomyces glabratus CBS 138 GenBank GCA_000002545.2 yes 0 0 13 Nakaseomyces glabratus CBS 138 FungiDB 5478.0 GCF_000002545.3_ASM254v2 GCA_000002545.2 GCF_000002545.3 False Nakaseomyces glabratus budding yeast N.glabratus (CBS 138 2008 refseq) https://genome.ucsc.edu/h/GCF_000002545.3 Encephalitozoon cuniculi GB-M1 GenBank GCA_000091225.2 yes 0 0 11 Encephalitozoon cuniculi GB-M1 MicrosporidiaDB 284813.0 GCF_000091225.2_ASM9122v2 GCA_000091225.2 GCF_000091225.2 True Encephalitozoon cuniculi GB-M1 microsporidians E.cuniculi (v2 GB-M1 2017) https://genome.ucsc.edu/h/GCF_000091225.2 Porospora cf. gigantea A INSDC GCA_019968955.1 yes 0 787 0 Porospora gigantea A CryptoDB 2853593.0 GCF_019968955.1_MNHN_PgigA_v1 GCA_019968955.1 GCF_019968955.1 True Porospora cf. gigantea A apicomplexans P.cf. gigantea (A 2021) https://genome.ucsc.edu/h/GCF_019968955.1 +Acanthamoeba sp. SK_2022c INSDC GCA_027944975.1 no 0 20778 0 Acanthamoeba sp. SK_2022c AmoebaDB 2919603.0 GCA_027944975.1_ASM2794497v1 GCA_027944975.1 False Acanthamoeba sp. SK_2022c A.sp. (SK_2022c 2023) https://genome.ucsc.edu/h/GCA_027944975.1 +Acanthamoeba sp. SK_2022b INSDC GCA_027943245.1 no 0 1790 0 Acanthamoeba sp. SK_2022b AmoebaDB 2919604.0 GCA_027943245.1_ASM2794324v1 GCA_027943245.1 False Acanthamoeba sp. SK_2022b A.sp. (SK_2022b 2023) https://genome.ucsc.edu/h/GCA_027943245.1 +Acanthamoeba sp. SK_2022a INSDC GCA_027943295.1 no 0 2108 0 Acanthamoeba sp. SK_2022a AmoebaDB 2919605.0 GCA_027943295.1_ASM2794329v1 GCA_027943295.1 False Acanthamoeba sp. SK_2022a A.sp. (SK_2022a 2023) https://genome.ucsc.edu/h/GCA_027943295.1 Entamoeba histolytica HM-1:IMSS GenBank GCA_000208925.2 yes 0 1496 0 Entamoeba histolytica HM-1:IMSS AmoebaDB 294381.0 GCF_000208925.1_JCVI_ESG2_1.0 GCA_000208925.2 GCF_000208925.1 True Entamoeba histolytica HM-1:IMSS E.histolytica (HM-1:IMSS 2008) https://genome.ucsc.edu/h/GCF_000208925.1 Meyerozyma guilliermondii ATCC 6260 INSDC GCA_000149425.1 yes 0 9 0 Meyerozyma guilliermondii ATCC 6260 FungiDB 294746.0 GCF_000149425.1_ASM14942v1 GCA_000149425.1 GCF_000149425.1 True Meyerozyma guilliermondii ATCC 6260 budding yeast M.guilliermondii ATCC 6260 https://genome.ucsc.edu/h/GCF_000149425.1 Candida tropicalis MYA-3404 GenBank GCA_000006335.3 yes 0 23 0 Candida tropicalis MYA-3404 FungiDB 294747.0 GCF_000006335.3_ASM633v3 GCA_000006335.3 GCF_000006335.3 True Candida tropicalis MYA-3404 budding yeast C.tropicalis MYA-3404 https://genome.ucsc.edu/h/GCF_000006335.3 @@ -148,6 +153,7 @@ Aspergillus terreus NIH2624 GenBank GCA_000149615.1 yes 0 26 0 Aspergillus terre Aspergillus clavatus NRRL 1 GenBank GCA_000002715.1 yes 0 143 0 Aspergillus clavatus NRRL 1 FungiDB 344612.0 GCF_000002715.2_ASM271v1 GCA_000002715.1 GCF_000002715.2 True Aspergillus clavatus NRRL 1 ascomycetes A.clavatus NRRL 1 https://genome.ucsc.edu/h/GCF_000002715.2 Leishmania major strain Friedlin GenBank GCA_000002725.2 yes 0 0 36 Leishmania major strain Friedlin TriTrypDB 347515.0 GCF_000002725.2_ASM272v2 GCA_000002725.2 GCF_000002725.2 True Leishmania major strain Friedlin Leishmania major (Friedlin 2011 kinetoplastids refseq) https://genome.ucsc.edu/h/GCF_000002725.2 Plasmodium yoelii yoelii 17XNL GenBank GCA_000003085.2 no 5617 0 0 Plasmodium yoelii yoelii 17XNL PlasmoDB 73239.0 GCF_000003085.2_ASM308v2 GCA_000003085.2 GCF_000003085.2 True Plasmodium yoelii yoelii apicomplexans P.yoelii yoelii (17XNL 2002) https://genome.ucsc.edu/h/GCF_000003085.2 +Cryptosporidium hominis TU502 GenBank GCA_000006425.1 yes 1422 0 0 Cryptosporidium hominis TU502 CryptoDB 353151.0 GCF_000006425.1_ASM642v1 GCA_000006425.1 GCF_000006425.1 True Cryptosporidium hominis TU502 apicomplexans C.hominis (TU502 2004 refseq) https://genome.ucsc.edu/h/GCF_000006425.1 Cryptosporidium parvum Iowa II GenBank GCA_000165345.1 yes 0 0 8 Cryptosporidium parvum Iowa II CryptoDB 353152.0 GCF_000165345.1_ASM16534v1 GCA_000165345.1 GCF_000165345.1 True Cryptosporidium parvum Iowa II apicomplexans C.parvum (Iowa type II 2007) https://genome.ucsc.edu/h/GCF_000165345.1 Trypanosoma cruzi strain CL Brener GenBank GCA_000209065.1 no 29407 0 0 Trypanosoma cruzi strain CL Brener TriTrypDB 5693.0 GCF_000209065.1_ASM20906v1 GCA_000209065.1 GCF_000209065.1 True Trypanosoma cruzi Trypanosoma cruzi (CL Brener 2005 kinetoplastids) https://genome.ucsc.edu/h/GCF_000209065.1 Plasmodium falciparum 3D7 GenBank GCA_000002765.3 yes 0 0 14 Plasmodium falciparum 3D7 PlasmoDB 36329.0 GCF_000002765.5_GCA_000002765 GCA_000002765.3 GCF_000002765.5 False Plasmodium falciparum 3D7 malaria parasite P. falciparum (3D7 2016 refseq) https://genome.ucsc.edu/h/GCF_000002765.5 @@ -162,6 +168,7 @@ Pseudocercospora fijiensis CIRAD86 INSDC GCA_000340215.1 yes 0 56 0 Pseudocercos Ascosphaera apis ARSEF 7405 INSDC GCA_001636715.1 yes 0 82 0 Ascosphaera apis ARSEF 7405 FungiDB 392613.0 GCA_001636715.1_AAP_1.0 GCA_001636715.1 False Ascosphaera apis ARSEF 7405 ascomycetes A.apis (ARSEF 7405 2016) https://genome.ucsc.edu/h/GCA_001636715.1 Coccidioides immitis H538.4 GenBank GCA_000149815.1 no 0 553 0 Coccidioides immitis H538.4 FungiDB 396776.0 GCA_000149815.1_ASM14981v1 GCA_000149815.1 False Coccidioides immitis H538.4 ascomycetes C.immitis (H538.4 2006) https://genome.ucsc.edu/h/GCA_000149815.1 Schizosaccharomyces japonicus yFS275 GenBank GCA_000149845.2 yes 0 32 0 Schizosaccharomyces japonicus yFS275 FungiDB 402676.0 GCF_000149845.2_SJ5 GCA_000149845.2 GCF_000149845.2 True Schizosaccharomyces japonicus yFS275 ascomycetes S.japonicus yFS275 https://genome.ucsc.edu/h/GCF_000149845.2 +Batrachochytrium dendrobatidis JEL423 GenBank GCA_000149865.1 yes 0 69 0 Batrachochytrium dendrobatidis JEL423 FungiDB 403673.0 GCA_000149865.1_BD_JEL423 GCA_000149865.1 False Batrachochytrium dendrobatidis JEL423 chytrids B.dendrobatidis (JEL423 2006) https://genome.ucsc.edu/h/GCA_000149865.1 Phytophthora infestans T30-4 GenBank GCA_000142945.1 yes 0 4921 0 Phytophthora infestans T30-4 FungiDB 403677.0 GCF_000142945.1_ASM14294v1 GCA_000142945.1 GCF_000142945.1 True Phytophthora infestans T30-4 potato late blight agent (T30-4 2009) https://genome.ucsc.edu/h/GCF_000142945.1 Coccidioides immitis RMSCC 2394 GenBank GCA_000149895.1 no 0 23 0 Coccidioides immitis RMSCC 2394 FungiDB 404692.0 GCA_000149895.1_ASM14989v1 GCA_000149895.1 False Coccidioides immitis RMSCC 2394 ascomycetes C.immitis (RMSCC 2394 2006) https://genome.ucsc.edu/h/GCA_000149895.1 Trichoderma virens Gv29-8 GenBank GCA_000170995.2 yes 93 0 0 Trichoderma virens Gv29-8 FungiDB 413071.0 GCF_000170995.1_TRIVI_v2.0 GCA_000170995.2 GCF_000170995.1 True Trichoderma virens Gv29-8 ascomycetes T.virens Gv29-8 https://genome.ucsc.edu/h/GCF_000170995.1 @@ -198,6 +205,7 @@ Coccidioides posadasii CPA 0066 GenBank GCA_000150645.1 no 0 473 0 Coccidioides Penicillium rubens Wisconsin 54-1255 GenBank GCA_000226395.1 yes 0 49 0 Penicillium rubens Wisconsin 54-1255 FungiDB 500485.0 GCF_000226395.1_PenChr_Nov2007 GCA_000226395.1 GCF_000226395.1 True Penicillium rubens Wisconsin 54-1255 ascomycetes P.rubens (Wisconsin 54-1255 2008 refseq) https://genome.ucsc.edu/h/GCF_000226395.1 Paracoccidioides lutzii Pb01 GenBank GCA_000150705.2 yes 0 110 0 Paracoccidioides lutzii Pb01 FungiDB 502779.0 GCF_000150705.2_Paracocci_br_Pb01_V2 GCA_000150705.2 GCF_000150705.2 True Paracoccidioides lutzii Pb01 ascomycetes P.lutzii Pb01 https://genome.ucsc.edu/h/GCF_000150705.2 Paracoccidioides brasiliensis Pb18 GenBank GCA_000150735.2 no 0 57 0 Paracoccidioides brasiliensis Pb18 FungiDB 502780.0 GCF_000150735.1_Paracocci_br_Pb18_V2 GCA_000150735.2 GCF_000150735.1 True Paracoccidioides brasiliensis Pb18 ascomycetes P.brasiliensis Pb18 https://genome.ucsc.edu/h/GCF_000150735.1 +Toxoplasma gondii GT1 GenBank GCA_000149715.2 no 2034 0 14 Toxoplasma gondii GT1 ToxoDB 507601.0 GCA_000149715.2_TGGT1 GCA_000149715.2 False Toxoplasma gondii GT1 apicomplexans T.gondii (GT1 2013) https://genome.ucsc.edu/h/GCA_000149715.2 Toxoplasma gondii ME49 GenBank GCF_000006565.2 yes 0 2248 14 Toxoplasma gondii ME49 ToxoDB 508771.0 GCF_000006565.2_TGA4 GCA_000006565.2 GCF_000006565.2 False Toxoplasma gondii ME49 Toxoplasma gondii (ME49 2013) https://genome.ucsc.edu/h/GCF_000006565.2 Aspergillus oryzae RIB40 GenBank GCA_000184455.3 yes 3 0 8 Aspergillus oryzae RIB40 FungiDB 510516.0 GCF_000184455.2_ASM18445v3 GCA_000184455.3 GCF_000184455.2 True Aspergillus oryzae RIB40 ascomycetes A.oryzae RIB40 https://genome.ucsc.edu/h/GCF_000184455.2 Neurospora tetrasperma FGSC 2508 GenBank GCA_000213175.1 yes 0 81 0 Neurospora tetrasperma FGSC 2508 FungiDB 510951.0 GCF_000213175.1_v2.0 GCA_000213175.1 GCF_000213175.1 True Neurospora tetrasperma FGSC 2508 ascomycetes N.tetrasperma FGSC 2508 https://genome.ucsc.edu/h/GCF_000213175.1 @@ -208,6 +216,7 @@ Histoplasma capsulatum H143 GenBank GCA_000151035.1 no 0 48 0 Histoplasma capsul Microsporum canis CBS 113480 INSDC GCA_000151145.1 yes 0 16 0 Microsporum canis CBS 113480 FungiDB 554155.0 GCF_000151145.1_ASM15114v1 GCA_000151145.1 GCF_000151145.1 True Microsporum canis CBS 113480 ascomycetes M.canis CBS 113480 https://genome.ucsc.edu/h/GCF_000151145.1 Saccharomyces cerevisiae S288C GenBank GCA_000146045.2 yes 0 0 16 Saccharomyces cerevisiae S288C FungiDB 559292.0 GCF_000146045.2_R64 GCA_000146045.2 GCF_000146045.2 False Saccharomyces cerevisiae S288C baker's yeast S288C (2014) https://genome.ucsc.edu/h/GCF_000146045.2 Blastomyces dermatitidis ER-3 INSDC GCA_000003525.2 yes 0 25 0 Blastomyces dermatitidis ER-3 FungiDB 559297.0 GCF_000003525.1_BD_ER3_V1 GCA_000003525.2 GCF_000003525.1 True Blastomyces dermatitidis ER-3 ascomycetes B.dermatitidis (ER-3 2009 refseq) https://genome.ucsc.edu/h/GCF_000003525.1 +Blastomyces gilchristii SLH14081 INSDC GCA_000003855.2 yes 0 100 0 Blastomyces gilchristii SLH14081 FungiDB 559298.0 GCF_000003855.2_BD_SLH14081_V1 GCA_000003855.2 GCF_000003855.2 True Blastomyces gilchristii SLH14081 ascomycetes B.gilchristii (SLH14081 2009 refseq) https://genome.ucsc.edu/h/GCF_000003855.2 Trichophyton rubrum CBS 118892 INSDC GCA_000151425.1 yes 0 35 0 Trichophyton rubrum CBS 118892 FungiDB 559305.0 GCF_000151425.1_ASM15142v1 GCA_000151425.1 GCF_000151425.1 True Trichophyton rubrum CBS 118892 ascomycetes T.rubrum CBS 118892 https://genome.ucsc.edu/h/GCF_000151425.1 Trichophyton equinum CBS 127.97 INSDC GCA_000151175.1 yes 0 123 0 Trichophyton equinum CBS 127.97 FungiDB 559882.0 GCA_000151175.1_ASM15117v1 GCA_000151175.1 False Trichophyton equinum CBS 127.97 ascomycetes T.equinum (CBS 127.97 2008) https://genome.ucsc.edu/h/GCA_000151175.1 Neospora caninum Liverpool GenBank GCA_000208865.2 yes 52 0 14 Neospora caninum Liverpool ToxoDB 572307.0 GCF_000208865.1_ASM20886v2 GCA_000208865.2 GCF_000208865.1 True Neospora caninum Liverpool apicomplexans N.caninum (Liverpool 2011) https://genome.ucsc.edu/h/GCF_000208865.1 @@ -219,6 +228,7 @@ Tremella mesenterica DSM 1558 GenBank GCA_000271645.1 yes 0 45 0 Tremella mesent Schizophyllum commune H4-8 INSDC GCA_000143185.2 yes 0 25 0 Schizophyllum commune H4-8 FungiDB 578458.0 GCF_000143185.2_Schco3 GCA_000143185.2 GCF_000143185.2 True Schizophyllum commune H4-8 basidiomycetes S.commune (v2 H4-8 2022) https://genome.ucsc.edu/h/GCF_000143185.2 Nosema ceranae BRL01 GenBank GCA_000182985.1 yes 5465 0 0 Nosema ceranae BRL01 MicrosporidiaDB 578460.0 GCF_000182985.1_ASM18298v1 GCA_000182985.1 GCF_000182985.1 True Nosema ceranae BRL01 microsporidians N.ceranae (BRL01 2009) https://genome.ucsc.edu/h/GCF_000182985.1 Nosema bombycis CQ1 GenBank GCA_000383075.1 yes 0 1607 0 Nosema bombycis CQ1 MicrosporidiaDB 578461.0 GCA_000383075.1_NosBomCQ1_v1.0 GCA_000383075.1 False Nosema bombycis CQ1 microsporidians N.bombycis (CQ1 2013) https://genome.ucsc.edu/h/GCA_000383075.1 +Allomyces macrogynus ATCC 38327 GenBank GCA_000151295.1 yes 0 101 0 Allomyces macrogynus ATCC 38327 FungiDB 578462.0 GCA_000151295.1_A_macrogynus_V3 GCA_000151295.1 False Allomyces macrogynus ATCC 38327 blastocladiomycotan A.macrogynus (ATCC 38327 2010) https://genome.ucsc.edu/h/GCA_000151295.1 Plasmodium berghei ANKA GenBank GCA_900002375.2 yes 5 0 14 Plasmodium berghei ANKA PlasmoDB 5823.0 GCF_900002375.2_GCA_900002375 GCA_900002375.2 GCF_900002375.2 False Plasmodium berghei ANKA apicomplexans P.berghei (ANKA 2019) https://genome.ucsc.edu/h/GCF_900002375.2 Plasmodium falciparum NF54 INSDC GCA_009761475.1 no 0 28 0 Plasmodium falciparum NF54 PlasmoDB 5833.0 GCA_009761475.1_NF54_v1 GCA_009761475.1 False Plasmodium falciparum malaria parasite P. falciparum (NF54 2019) https://genome.ucsc.edu/h/GCA_009761475.1 Plasmodium knowlesi strain H GenBank GCA_000006355.3 yes 148 0 14 Plasmodium knowlesi strain H PlasmoDB 5851.0 GCF_000006355.2_GCA_000006355.2 GCA_000006355.3 GCF_000006355.2 False Plasmodium knowlesi strain H apicomplexans P.knowlesi strain (H 2020) https://genome.ucsc.edu/h/GCF_000006355.2 @@ -256,12 +266,25 @@ Theileria orientalis strain Shintoku GenBank GCA_000740895.1 yes 0 0 4 Theileria Encephalitozoon intestinalis ATCC 50506 GenBank GCA_000146465.1 yes 0 0 11 Encephalitozoon intestinalis ATCC 50506 MicrosporidiaDB 876142.0 GCF_000146465.1_ASM14646v1 GCA_000146465.1 GCF_000146465.1 True Encephalitozoon intestinalis ATCC 50506 microsporidians E.intestinalis ATCC 50506 https://genome.ucsc.edu/h/GCF_000146465.1 Epichloe festucae Fl1 INSDC GCA_003814445.1 yes 0 0 7 Epichloe festucae Fl1 FungiDB 877507.0 GCA_003814445.1_ASM381444v1 GCA_003814445.1 False Epichloe festucae Fl1 ascomycetes E.festucae (Fl1 2018) https://genome.ucsc.edu/h/GCA_003814445.1 Nematocida parisii ERTm1 GenBank GCA_000250985.1 yes 0 65 0 Nematocida parisii ERTm1 MicrosporidiaDB 881290.0 GCF_000250985.1_Nema_parisii_ERTm1_V3 GCA_000250985.1 GCF_000250985.1 True Nematocida parisii ERTm1 microsporidians N.parisii ERTm1 https://genome.ucsc.edu/h/GCF_000250985.1 +Entamoeba histolytica DS4-868 INSDC GCA_018466815.1 no 0 1177 0 Entamoeba histolytica DS4-868 AmoebaDB 885310.0 GCA_018466815.1_ASM1846681v1 GCA_018466815.1 False Entamoeba histolytica DS4-868 E.histolytica (DS4-868 2021) https://genome.ucsc.edu/h/GCA_018466815.1 +Entamoeba histolytica KU27 GenBank GCA_000338855.1 no 0 1796 0 Entamoeba histolytica KU27 AmoebaDB 885311.0 GCA_000338855.1_EHA_ku27_v1 GCA_000338855.1 False Entamoeba histolytica KU27 E.histolytica (KU27 2013) https://genome.ucsc.edu/h/GCA_000338855.1 +Entamoeba histolytica KU48 INSDC GCA_019059535.1 no 0 1168 0 Entamoeba histolytica KU48 AmoebaDB 885312.0 GCA_019059535.1_ASM1905953v1 GCA_019059535.1 False Entamoeba histolytica KU48 E.histolytica (KU48 2021) https://genome.ucsc.edu/h/GCA_019059535.1 +Entamoeba histolytica KU50 INSDC GCA_020283535.1 no 0 1063 0 Entamoeba histolytica KU50 AmoebaDB 885313.0 GCA_020283535.1_ASM2028353v1 GCA_020283535.1 False Entamoeba histolytica KU50 E.histolytica (KU50 2021) https://genome.ucsc.edu/h/GCA_020283535.1 +Entamoeba histolytica HM-3:IMSS GenBank GCA_000346345.1 no 0 1880 0 Entamoeba histolytica HM-3:IMSS AmoebaDB 885315.0 GCA_000346345.1_EHA.strHM3_v1 GCA_000346345.1 False Entamoeba histolytica HM-3:IMSS E.histolytica (HM-3:IMSS 2013) https://genome.ucsc.edu/h/GCA_000346345.1 +Entamoeba histolytica HM-1:IMSS-A GenBank GCA_000365475.1 no 0 1685 0 Entamoeba histolytica HM-1:IMSS-A AmoebaDB 885318.0 GCA_000365475.1_EHA_CA_v1 GCA_000365475.1 False Entamoeba histolytica HM-1:IMSS-A E.histolytica (HM-1:IMSS-A 2013) https://genome.ucsc.edu/h/GCA_000365475.1 +Entamoeba histolytica HM-1:IMSS-B GenBank GCA_000344925.1 no 0 1938 0 Entamoeba histolytica HM-1:IMSS-B AmoebaDB 885319.0 GCA_000344925.1_EHA_CB_v1 GCA_000344925.1 False Entamoeba histolytica HM-1:IMSS-B E.histolytica (HM-1:IMSS-B 2013) https://genome.ucsc.edu/h/GCA_000344925.1 Encephalitozoon hellem ATCC 50504 GenBank GCA_000277815.3 yes 0 0 12 Encephalitozoon hellem ATCC 50504 MicrosporidiaDB 907965.0 GCF_000277815.2_ASM27781v3 GCA_000277815.3 GCF_000277815.2 True Encephalitozoon hellem ATCC 50504 microsporidians E.hellem ATCC 50504 https://genome.ucsc.edu/h/GCF_000277815.2 Trypanosoma cruzi JR cl. 4 GenBank GCA_000331405.1 no 14752 560 0 Trypanosoma cruzi JR cl. 4 TriTrypDB 914063.0 GCA_000331405.1_Trypanosoma_cruzi_JR_cl4-1.1.4 GCA_000331405.1 False Trypanosoma cruzi JR cl. 4 Trypanosoma cruzi (JR cl. 4 2013) https://genome.ucsc.edu/h/GCA_000331405.1 Leishmania mexicana MHOM/GT/2001/U1103 GenBank GCA_000234665.4 yes 554 0 34 Leishmania mexicana MHOM/GT/2001/U1103 TriTrypDB 929439.0 GCF_000234665.1_ASM23466v4 GCA_000234665.4 GCF_000234665.1 True Leishmania mexicana MHOM/GT/2001/U1103 Leishmania mexicana (MHOM/GT/2001/U1103 2011 kinetoplastids) https://genome.ucsc.edu/h/GCF_000234665.1 +Toxoplasma gondii VAND GenBank GCA_000224845.2 no 0 2137 0 Toxoplasma gondii VAND ToxoDB 933077.0 GCA_000224845.2_TGVAND_v2 GCA_000224845.2 False Toxoplasma gondii VAND apicomplexans T.gondii (VAND 2014) https://genome.ucsc.edu/h/GCA_000224845.2 +Toxoplasma gondii RUB GenBank GCA_000224805.2 no 0 2424 0 Toxoplasma gondii RUB ToxoDB 935652.0 GCA_000224805.2_TGRUB_v2 GCA_000224805.2 False Toxoplasma gondii RUB apicomplexans T.gondii (RUB 2014) https://genome.ucsc.edu/h/GCA_000224805.2 Nematocida parisii ERTm3 GenBank GCA_000190615.1 no 0 53 0 Nematocida parisii ERTm3 MicrosporidiaDB 935791.0 GCA_000190615.1_Nema_parisii_ERTm3_V1 GCA_000190615.1 False Nematocida parisii ERTm3 microsporidians N.parisii (ERTm3 2011) https://genome.ucsc.edu/h/GCA_000190615.1 +Toxoplasma gondii MAS GenBank GCA_000224865.2 no 0 2180 0 Toxoplasma gondii MAS ToxoDB 943118.0 GCA_000224865.2_TGMAS1_v2 GCA_000224865.2 False Toxoplasma gondii MAS apicomplexans T.gondii (MAS 2014) https://genome.ucsc.edu/h/GCA_000224865.2 +Toxoplasma gondii p89 GenBank GCA_000224885.2 no 0 2150 0 Toxoplasma gondii p89 ToxoDB 943119.0 GCA_000224885.2_TGP89A_v02 GCA_000224885.2 False Toxoplasma gondii p89 apicomplexans T.gondii (p89 2014) https://genome.ucsc.edu/h/GCA_000224885.2 +Toxoplasma gondii TgCATBr9 GenBank GCA_000224825.2 no 0 2452 0 Toxoplasma gondii TgCATBr9 ToxoDB 943120.0 GCA_000224825.2_TGCATBR9_v2 GCA_000224825.2 False Toxoplasma gondii TgCATBr9 apicomplexans T.gondii (TgCATBr9 2018) https://genome.ucsc.edu/h/GCA_000224825.2 Toxoplasma gondii TgCATBr5 GenBank GCA_000259835.1 no 6995 0 0 Toxoplasma gondii TgCATBr5 ToxoDB 943121.0 GCA_000259835.1_TGCATBR5 GCA_000259835.1 False Toxoplasma gondii TgCATBr5 apicomplexans T.gondii (TgCATBr5 2011) https://genome.ucsc.edu/h/GCA_000259835.1 Toxoplasma gondii CAST GenBank GCA_000256705.2 no 0 2656 0 Toxoplasma gondii CAST ToxoDB 943122.0 GCA_000256705.2_TGCAST_v2 GCA_000256705.2 False Toxoplasma gondii CAST apicomplexans T.gondii (CAST 2018) https://genome.ucsc.edu/h/GCA_000256705.2 +Toxoplasma gondii FOU GenBank GCA_000224905.2 no 0 2869 0 Toxoplasma gondii FOU ToxoDB 943167.0 GCA_000224905.2_TGFOU1v02 GCA_000224905.2 False Toxoplasma gondii FOU apicomplexans T.gondii (FOU 2014) https://genome.ucsc.edu/h/GCA_000224905.2 Vavraia culicis subsp. floridensis GenBank GCA_000192795.1 yes 0 379 0 Vavraia culicis subsp. floridensis MicrosporidiaDB 948595.0 GCF_000192795.1_Vavr_culi_floridensis_V1 GCA_000192795.1 GCF_000192795.1 True Vavraia culicis subsp. floridensis microsporidians V.culicis subsp. floridensis https://genome.ucsc.edu/h/GCF_000192795.1 Leishmania donovani BPK282A1 GenBank GCA_000227135.2 yes 0 0 36 Leishmania donovani BPK282A1 TriTrypDB 5661.0 GCF_000227135.1_ASM22713v2 GCA_000227135.2 GCF_000227135.1 True Leishmania donovani Leishmania donovani (BPK282A1 2011 kinetoplastids) https://genome.ucsc.edu/h/GCF_000227135.1 Cordyceps militaris CM01 INSDC GCA_000225605.1 no 0 32 0 Cordyceps militaris CM01 FungiDB 983644.0 GCF_000225605.1_CmilitarisCM01_v01 GCA_000225605.1 GCF_000225605.1 True Cordyceps militaris CM01 ascomycetes C.militaris CM01 https://genome.ucsc.edu/h/GCF_000225605.1 @@ -281,8 +304,12 @@ Anopheles aquasalis AaquGF1 INSDC GCF_943734665.1 yes 0 86 4 Anopheles aquasalis Anopheles arabiensis DONGOLA 2021 INSDC GCF_016920715.1 yes 0 98 3 Anopheles arabiensis DONGOLA 2021 VectorBase 7173.0 GCF_016920715.1_AaraD3 GCA_016920715.1 GCF_016920715.1 False Anopheles arabiensis mosquito A.arabiensis (DONGOLA 2021) https://genome.ucsc.edu/h/GCF_016920715.1 Anopheles arabiensis Dongola INSDC GCA_000349185.1 no 0 1214 0 Anopheles arabiensis Dongola VectorBase 7173.0 GCA_000349185.1_Anop_arab_DONG5_A_V1 GCA_000349185.1 False Anopheles arabiensis mosquito A.arabiensis (DONG5_A 2013) https://genome.ucsc.edu/h/GCA_000349185.1 Aphanomyces astaci strain APO3 GenBank GCA_000520075.1 yes 0 835 0 Aphanomyces astaci strain APO3 FungiDB 112090.0 GCF_000520075.1_Apha_asta_APO3_V1 GCA_000520075.1 GCF_000520075.1 True Aphanomyces astaci oomycetes (APO3 2014) https://genome.ucsc.edu/h/GCF_000520075.1 +Acanthamoeba astronyxis Unknown GenBank GCA_000826245.1 yes 0 98248 0 Acanthamoeba astronyxis Unknown AmoebaDB 65658.0 GCA_000826245.1_Acanthamoeba_astronyxis GCA_000826245.1 False Acanthamoeba astronyxis A.astronyxis (2015) https://genome.ucsc.edu/h/GCA_000826245.1 Anopheles atroparvus EBRO INSDC GCA_000473505.1 yes 0 1315 5 Anopheles atroparvus EBRO VectorBase 41427.0 GCA_000473505.1_Anop_atro_EBRO_V1 GCA_000473505.1 False Anopheles atroparvus mosquito A.atroparvus (EBRO 2013) https://genome.ucsc.edu/h/GCA_000473505.1 Anopheles bellator AbelBR1 INSDC GCF_943735745.2 yes 0 2982 3 Anopheles bellator AbelBR1 VectorBase 139047.0 GCF_943735745.2_idAnoBellAS_SP24_06.2 GCA_943735745.2 GCF_943735745.2 False Anopheles bellator mosquito A.bellator (2023) https://genome.ucsc.edu/h/GCF_943735745.2 +Acanthamoeba castellanii C3 INSDC GCA_021020595.1 no 0 174 0 Acanthamoeba castellanii C3 AmoebaDB 5755.0 GCA_021020595.1_ASM2102059v1 GCA_021020595.1 False Acanthamoeba castellanii A.castellanii (C3 2021) https://genome.ucsc.edu/h/GCA_021020595.1 +Acanthamoeba castellanii Ma GenBank GCA_000826485.1 no 0 221748 0 Acanthamoeba castellanii Ma AmoebaDB 5755.0 GCA_000826485.1_Acanthamoeba_castellanii GCA_000826485.1 False Acanthamoeba castellanii A.castellanii (2015) https://genome.ucsc.edu/h/GCA_000826485.1 +Acanthamoeba castellanii str. Neff 2021 INSDC GCA_021020605.1 no 0 111 0 Acanthamoeba castellanii str. Neff 2021 AmoebaDB 5755.0 GCA_021020605.1_ASM2102060v1 GCA_021020605.1 False Acanthamoeba castellanii A.castellanii (Neff 2021) https://genome.ucsc.edu/h/GCA_021020605.1 Anopheles christyi ACHKN1017 INSDC GCA_000349165.1 yes 0 30369 0 Anopheles christyi ACHKN1017 VectorBase 43041.0 GCA_000349165.1_Anop_chri_ACHKN1017_V1 GCA_000349165.1 False Anopheles christyi mosquito A.christyi (ACHKN1017 2013) https://genome.ucsc.edu/h/GCA_000349165.1 Anopheles coluzzii AcolN3 INSDC GCF_943734685.1 yes 0 125 3 Anopheles coluzzii AcolN3 VectorBase 1518534.0 GCF_943734685.1_AcolN3 GCA_943734685.1 GCF_943734685.1 True Anopheles coluzzii mosquito A.coluzzii (primary hap 2022) https://genome.ucsc.edu/h/GCF_943734685.1 Anopheles coluzzii MOPTI INSDC GCF_016920705.1 no 0 196 3 Anopheles coluzzii MOPTI VectorBase 1518534.0 GCF_016920705.1_AcolMOP1 GCA_016920705.1 GCF_016920705.1 False Anopheles coluzzii mosquito A.coluzzi (MOPTI 2021) https://genome.ucsc.edu/h/GCF_016920705.1 @@ -290,7 +317,11 @@ Anopheles coluzzii Mali-NIH INSDC GCA_000150765.1 no 0 10521 0 Anopheles coluzzi Anopheles coustani AcouGA1 INSDC GCF_943734705.1 yes 0 416 3 Anopheles coustani AcouGA1 VectorBase 139045.0 GCF_943734705.1_idAnoCousDA_361_x.2 GCA_943734705.2 GCF_943734705.1 False Anopheles coustani mosquito A.coustani (2023) https://genome.ucsc.edu/h/GCF_943734705.1 Aspergillus cristatus GZAAS20.1005 INSDC GCA_001717485.1 yes 0 68 0 Aspergillus cristatus GZAAS20.1005 FungiDB 573508.0 GCA_001717485.1_ASM171748v1 GCA_001717485.1 False Aspergillus cristatus ascomycetes A.cristatus (GZAAS20.1005 2016) https://genome.ucsc.edu/h/GCA_001717485.1 Anopheles cruzii AcruBR1 INSDC GCF_943734635.1 yes 0 5085 3 Anopheles cruzii AcruBR1 VectorBase 68878.0 GCF_943734635.1_idAnoCruzAS_RS32_06 GCA_943734635.1 GCF_943734635.1 False Anopheles cruzii mosquito A.cruzii (2022) https://genome.ucsc.edu/h/GCF_943734635.1 +Acanthamoeba sp Galka GenBank GCA_000826505.1 yes 0 224137 0 Acanthamoeba sp. Galka AmoebaDB 65662.0 GCA_000826505.1_Acanthamoeba_pearcei GCA_000826505.1 False Acanthamoeba pearcei A.pearcei (2015) https://genome.ucsc.edu/h/GCA_000826505.1 +Acanthamoeba sp Incertae sedis GenBank GCA_000826365.1 no 0 24098 0 Acanthamoeba sp. Incertae_sedis AmoebaDB 32600.0 GCA_000826365.1_Acanthamoeba_royreba GCA_000826365.1 False Acanthamoeba royreba A.royreba (2015) https://genome.ucsc.edu/h/GCA_000826365.1 +Acanthamoeba sp T4b-type GenBank GCA_000826345.1 no 0 224482 0 Acanthamoeba sp. T4B-type AmoebaDB 5757.0 GCA_000826345.1_Acanthamoeba_polyphaga GCA_000826345.1 False Acanthamoeba polyphaga A.polyphaga (2015) https://genome.ucsc.edu/h/GCA_000826345.1 Anopheles culicifacies A-37 INSDC GCA_000473375.1 yes 0 16162 0 Anopheles culicifacies A-37 VectorBase 139723.0 GCA_000473375.1_Anop_culi_species_A-37_1_V1 GCA_000473375.1 False Anopheles culicifacies mosquito A.culicifacies (species A-37_1 2013) https://genome.ucsc.edu/h/GCA_000473375.1 +Acanthamoeba culbertsoni A1 GenBank GCA_000826265.1 yes 0 72411 0 Acanthamoeba culbertsoni A1 AmoebaDB 43142.0 GCA_000826265.1_Acanthamoeba_culbertsoni_genome_assembly GCA_000826265.1 False Acanthamoeba culbertsoni A.culbertsoni (2015) https://genome.ucsc.edu/h/GCA_000826265.1 Anopheles darlingi AdarGF1 INSDC GCF_943734745.1 yes 0 62 3 Anopheles darlingi AdarGF1 VectorBase 43151.0 GCF_943734745.1_idAnoDarlMG_H_01 GCA_943734745.1 GCF_943734745.1 True Anopheles darlingi American malaria mosquito (primary hap 2022) https://genome.ucsc.edu/h/GCF_943734745.1 Anopheles darlingi Coari INSDC GCA_000211455.3 no 0 2220 0 Anopheles darlingi Coari VectorBase 43151.0 GCA_000211455.3_A_darlingi_v1 GCA_000211455.3 False Anopheles darlingi American malaria mosquito (2013) https://genome.ucsc.edu/h/GCA_000211455.3 Angomonas deanei strain Cavalho ATCC PRA-265 INSDC GCA_903995115.1 yes 0 0 29 Angomonas deanei strain Cavalho ATCC PRA-265 TriTrypDB 59799.0 GCA_903995115.1_Adeanei_nanopore_chromosomes GCA_903995115.1 False Angomonas deanei Angomonas (Crithidia deanei Carvalho ATCC PRA-265 2020) https://genome.ucsc.edu/h/GCA_903995115.1 @@ -305,11 +336,14 @@ Anopheles gambiae Ifakara INSDC GCF_943734735.2 no 0 187 3 Anopheles gambiae Ifa Anopheles gambiae Pimperena INSDC GCA_000150785.1 no 0 13042 0 Anopheles gambiae Pimperena VectorBase 7165.0 GCA_000150785.1_g4 GCA_000150785.1 False Anopheles gambiae African malaria mosquito (S 2008) https://genome.ucsc.edu/h/GCA_000150785.1 Aphanomyces invadans NJM9701 GenBank GCA_000520115.1 yes 0 481 0 Aphanomyces invadans NJM9701 FungiDB 157072.0 GCF_000520115.1_Apha_inva_NJM9701_V1 GCA_000520115.1 GCF_000520115.1 True Aphanomyces invadans oomycetes (NJM9701 2014) https://genome.ucsc.edu/h/GCF_000520115.1 Aspergillus lentulus strain IFM 54703 INSDC GCA_001445615.2 yes 0 12 0 Aspergillus lentulus strain IFM 54703 FungiDB 293939.0 GCA_001445615.2_Alt_assembly01 GCA_001445615.2 False Aspergillus lentulus ascomycetes A.lentulus (IFM 54703 2021) https://genome.ucsc.edu/h/GCA_001445615.2 +Acanthamoeba lenticulata PD2S GenBank GCA_000826285.1 yes 0 79048 0 Acanthamoeba lenticulata PD2S AmoebaDB 29196.0 GCA_000826285.1_Acanthamoeba_lenticulata GCA_000826285.1 False Acanthamoeba lenticulata A.lenticulata (2015) https://genome.ucsc.edu/h/GCA_000826285.1 Antonospora locustae CLX INSDC GCA_007674295.1 yes 0 1 17 Antonospora locustae CLX MicrosporidiaDB 278021.0 GCA_007674295.1_ASM767429v1 GCA_007674295.1 False Antonospora locustae microsporidians A.locustae (CLX 2019) https://genome.ucsc.edu/h/GCA_007674295.1 +Acanthamoeba lugdunensis L3a GenBank GCA_000826425.1 yes 0 67459 0 Acanthamoeba lugdunensis L3a AmoebaDB 61605.0 GCA_000826425.1_Acanthamoeba_lugdunensis GCA_000826425.1 False Acanthamoeba lugdunensis A.lugdunensis (2015) https://genome.ucsc.edu/h/GCA_000826425.1 Anopheles maculipalpis AmacGA1 INSDC GCF_943734695.1 yes 0 167 3 Anopheles maculipalpis AmacGA1 VectorBase 1496333.0 GCF_943734695.1_idAnoMacuDA_375_x GCA_943734695.1 GCF_943734695.1 True Anopheles maculipalpis mosquito A.maculipalpis (primary hap 2022) https://genome.ucsc.edu/h/GCF_943734695.1 Amblyomma maculatum SK-2019 INSDC GCA_023969395.1 yes 0 125877 0 Amblyomma maculatum SK-2019 VectorBase 34609.0 GCA_023969395.1_ASM2396939v1 GCA_023969395.1 False Amblyomma maculatum Gulf Coast tick (SK-2019 2022) https://genome.ucsc.edu/h/GCA_023969395.1 Anopheles maculatus maculatus3 INSDC GCA_000473185.1 yes 0 47797 0 Anopheles maculatus maculatus3 VectorBase 74869.0 GCA_000473185.1_Anop_macu_maculatus3_V1 GCA_000473185.1 False Anopheles maculatus mosquito A.maculatus (maculatus3 2013) https://genome.ucsc.edu/h/GCA_000473185.1 Anopheles marshallii AmarGA1 INSDC GCF_943734725.1 yes 0 285 3 Anopheles marshallii AmarGA1 VectorBase 1521116.0 GCF_943734725.1_idAnoMarsDA_429_01 GCA_943734725.1 GCF_943734725.1 True Anopheles marshallii mosquito A.marshallii (primary hap 2022) https://genome.ucsc.edu/h/GCF_943734725.1 +Acanthamoeba mauritaniensis 1652 GenBank GCA_000826465.1 yes 0 67233 0 Acanthamoeba mauritaniensis 1652 AmoebaDB 196912.0 GCA_000826465.1_Acanthamoeba_mauritaniensis GCA_000826465.1 False Acanthamoeba mauritaniensis A.mauritaniensis (2015) https://genome.ucsc.edu/h/GCA_000826465.1 Anopheles melas CM1001059_A INSDC GCA_000473525.2 yes 0 20229 0 Anopheles melas CM1001059_A VectorBase 34690.0 GCA_000473525.2_Anop_mela_CM1001059_A_V2 GCA_000473525.2 False Anopheles melas mosquito A.melas (CM1001059_A 2014) https://genome.ucsc.edu/h/GCA_000473525.2 Anopheles merus MAF INSDC GCA_000473845.2 no 0 2027 0 Anopheles merus MAF VectorBase 30066.0 GCA_000473845.2_Anop_meru_MAF_V1 GCA_000473845.2 False Anopheles merus mosquito A.merus (MAF 2014) https://genome.ucsc.edu/h/GCA_000473845.2 Anopheles merus MAF 2021 INSDC GCF_017562075.2 yes 0 1322 5 Anopheles merus MAF 2021 VectorBase 30066.0 GCF_017562075.2_AmerM5.1 GCA_017562075.2 GCF_017562075.2 False Anopheles merus mosquito A.merus (MAF 2021) https://genome.ucsc.edu/h/GCF_017562075.2 @@ -321,8 +355,11 @@ Aspergillus niger strain LDM3 INSDC GCA_009812365.1 no 0 14 0 Aspergillus niger Aspergillus niger strain N402 (ATCC64974) GenBank GCA_900248155.1 no 19 0 0 Aspergillus niger strain N402 (ATCC64974) FungiDB 5061.0 GCA_900248155.1_Aniger_ATCC_64974_N402 GCA_900248155.1 False Aspergillus niger ascomycetes A.niger (N402 ATCC 64974 2018) https://genome.ucsc.edu/h/GCA_900248155.1 Amauroascus niger isolate UAMH 3544 GenBank GCA_001430945.1 yes 3481 0 0 Amauroascus niger isolate UAMH 3544 FungiDB 89421.0 GCA_001430945.1_ASM143094v1 GCA_001430945.1 False Amauroascus niger ascomycetes A.niger (UAMH 3544 2015) https://genome.ucsc.edu/h/GCA_001430945.1 Anopheles nili AnilCM1 INSDC GCF_943737925.1 yes 0 153 3 Anopheles nili AnilCM1 VectorBase 185578.0 GCF_943737925.1_idAnoNiliSN_F5_01 GCA_943737925.1 GCF_943737925.1 True Anopheles nili mosquito A.nili (primary hap 2022) https://genome.ucsc.edu/h/GCF_943737925.1 +Acanthamoeba palestinensis Reich GenBank GCA_000826305.1 yes 0 26188 0 Acanthamoeba palestinensis Reich AmoebaDB 65661.0 GCA_000826305.1_Acanthamoeba_healyi GCA_000826305.1 False Acanthamoeba healyi A.healyi (2015) https://genome.ucsc.edu/h/GCA_000826305.1 Aspergillus parasiticus CBS 117618 INSDC GCA_009176385.1 yes 0 270 0 Aspergillus parasiticus CBS 117618 FungiDB 5067.0 GCA_009176385.1_Asppar1 GCA_009176385.1 False Aspergillus parasiticus ascomycetes A.parasiticus (CBS 117618 2019) https://genome.ucsc.edu/h/GCA_009176385.1 Anopheles quadriannulatus SANGWE INSDC GCA_000349065.1 yes 0 2823 0 Anopheles quadriannulatus SANGWE VectorBase 34691.0 GCA_000349065.1_Anop_quad_QUAD4_A_V1 GCA_000349065.1 False Anopheles quadriannulatus mosquito A.quadriannulatus (QUAD4_A 2013) https://genome.ucsc.edu/h/GCA_000349065.1 +Acanthamoeba quina Vil3 GenBank GCA_000826445.1 yes 0 60490 0 Acanthamoeba quina Vil3 AmoebaDB 211522.0 GCA_000826445.1_Acanthamoeba_quina GCA_000826445.1 False Acanthamoeba quina A.quina (2015) https://genome.ucsc.edu/h/GCA_000826445.1 +Acanthamoeba rhysodes Singh GenBank GCA_000826385.1 yes 0 62836 0 Acanthamoeba rhysodes Singh AmoebaDB 32599.0 GCA_000826385.1_Acanthamoeba_rhysodes GCA_000826385.1 False Acanthamoeba rhysodes A.rhysodes (2015) https://genome.ucsc.edu/h/GCA_000826385.1 Anopheles sinensis China INSDC GCA_000441895.2 yes 0 9592 0 Anopheles sinensis China VectorBase 74873.0 GCA_000441895.2_AS2 GCA_000441895.2 False Anopheles sinensis mosquito A.sinensis (2014) https://genome.ucsc.edu/h/GCA_000441895.2 Anopheles sinensis SINENSIS INSDC GCA_000472065.2 no 0 10448 0 Anopheles sinensis SINENSIS VectorBase 74873.0 GCA_000472065.2_Anop_sine_SINENSIS_V1 GCA_000472065.2 False Anopheles sinensis mosquito A.sinensis (SINENSIS 2014) https://genome.ucsc.edu/h/GCA_000472065.2 Anopheles stephensi Indian INSDC GCA_000300775.2 no 0 23371 0 Anopheles stephensi Indian VectorBase 30069.0 GCA_000300775.2_ASM30077v2 GCA_000300775.2 False Anopheles stephensi Asian malaria mosquito (Indian Wild Type Walter Reed 2013) https://genome.ucsc.edu/h/GCA_000300775.2 @@ -330,6 +367,7 @@ Anopheles stephensi SDA-500 INSDC GCA_000349045.1 no 0 1110 0 Anopheles stephens Anopheles stephensi UCISS2018 INSDC GCF_013141755.1 yes 0 491 3 Anopheles stephensi UCISS2018 VectorBase 30069.0 GCF_013141755.1_UCI_ANSTEP_V1.0 GCA_013141755.1 GCF_013141755.1 False Anopheles stephensi Asian malaria mosquito https://genome.ucsc.edu/h/GCF_013141755.1 Aspergillus tanneri NIH1004 INSDC GCA_004798825.1 yes 0 1715 0 Aspergillus tanneri NIH1004 FungiDB 1220188.0 GCA_004798825.1_ASM479882v1 GCA_004798825.1 False Aspergillus tanneri ascomycetes A.tanneri (NIH1004 2019) https://genome.ucsc.edu/h/GCA_004798825.1 Aspergillus thermomutatus strain HMR AF 39 INSDC GCA_002237265.2 yes 0 647 0 Aspergillus thermomutatus strain HMR AF 39 FungiDB 41047.0 GCF_002237265.1_ASM223726v2 GCA_002237265.2 GCF_002237265.1 True Aspergillus thermomutatus ascomycetes A.thermomutatus https://genome.ucsc.edu/h/GCF_002237265.1 +Acanthamoeba triangularis SH621 GenBank GCA_000826325.1 yes 0 56742 0 Acanthamoeba triangularis SH621 AmoebaDB 28015.0 GCA_000826325.1_Acanthamoeba_palestinensis GCA_000826325.1 False Acanthamoeba palestinensis A.palestinensis (2015) https://genome.ucsc.edu/h/GCA_000826325.1 Apophysomyces variabilis NCCPF 102052 INSDC GCA_002749535.1 yes 0 411 0 Apophysomyces variabilis NCCPF 102052 FungiDB 760013.0 GCA_002749535.1_ASM274953v1 GCA_002749535.1 False Apophysomyces variabilis fungi A.variabilis (NCCPF 102052 2017) https://genome.ucsc.edu/h/GCA_002749535.1 Anopheles ziemanni AzieGA1 INSDC GCF_943734765.1 yes 0 416 3 Anopheles ziemanni AzieGA1 VectorBase 345580.0 GCF_943734765.1_idAnoZiCoDA_A2_x.2 GCA_943734765.2 GCF_943734765.1 False Anopheles ziemanni mosquito A.ziemanni (2023) https://genome.ucsc.edu/h/GCF_943734765.1 Blechomonas ayalai B08-376 GenBank GCA_020509355.1 yes 0 545 0 Blechomonas ayalai B08-376 TriTrypDB 1463230.0 GCA_020509355.1_ASM2050935v1 GCA_020509355.1 False Blechomonas ayalai Blechomonas ayalai (B08-376 2021) https://genome.ucsc.edu/h/GCA_020509355.1 @@ -345,6 +383,8 @@ Babesia duncani strain WA1 2023 INSDC GCA_028658345.1 yes 0 160 5 Babesia duncan Biomphalaria glabrata XG47 INSDC GCF_947242115.1 yes 0 25 18 Biomphalaria glabrata XG47 VectorBase 6526.0 GCF_947242115.1_xgBioGlab47.1 GCA_947242115.1 GCF_947242115.1 False Biomphalaria glabrata bloodfluke planorb (primary hap 2022) https://genome.ucsc.edu/h/GCF_947242115.1 Blumeria graminis f. sp. triticale THUN-12 INSDC GCA_905067625.1 no 0 25 11 Blumeria graminis f. sp. triticale THUN-12 FungiDB 1689686.0 GCA_905067625.1_Bgtriticale_THUN12_genome_v1_2 GCA_905067625.1 False Blumeria graminis f. sp. triticale grass mildew (THUN-12 2021) https://genome.ucsc.edu/h/GCA_905067625.1 Blumeria hordei strain RACE1 INSDC GCA_900237765.1 yes 0 99 0 Blumeria hordei strain RACE1 FungiDB 2867405.0 GCA_900237765.1_BghRACE1_v1 GCA_900237765.1 False Blumeria hordei grass mildew (RACE1 RACE1 2018) https://genome.ucsc.edu/h/GCA_900237765.1 +Balamuthia mandrillaris strain 2046 INSDC GCA_001262475.1 no 0 14699 0 Balamuthia mandrillaris strain 2046 AmoebaDB 66527.0 GCA_001262475.1_ASM126247v1 GCA_001262475.1 False Balamuthia mandrillaris B.mandrillaris (2046 2015) https://genome.ucsc.edu/h/GCA_001262475.1 +Balamuthia mandrillaris CDC-V039 INSDC GCA_001185145.1 yes 0 1604 0 Balamuthia mandrillaris CDC-V039 AmoebaDB 66527.0 GCA_001185145.1_ASM118514v1 GCA_001185145.1 False Balamuthia mandrillaris B.mandrillaris (CDC-V039 2015) https://genome.ucsc.edu/h/GCA_001185145.1 Babesia microti strain ATCC 30222 INSDC GCA_001650055.1 no 234 0 0 Babesia microti strain ATCC 30222 PiroplasmaDB 5868.0 GCA_001650055.1_ASM165005v1 GCA_001650055.1 False Babesia microti apicomplexans B.microti (ATCC 30222 2016) https://genome.ucsc.edu/h/GCA_001650055.1 Babesia microti strain GI INSDC GCA_001650105.1 no 140 0 0 Babesia microti strain GI PiroplasmaDB 5868.0 GCA_001650105.1_ASM165010v1 GCA_001650105.1 False Babesia microti apicomplexans B.microti (GI 2016) https://genome.ucsc.edu/h/GCA_001650105.1 Babesia microti strain GreenwichYale_Lab_strain_1 INSDC GCA_001650075.1 no 250 0 0 Babesia microti strain GreenwichYale_Lab_strain_1 PiroplasmaDB 5868.0 GCA_001650075.1_ASM165007v1 GCA_001650075.1 False Babesia microti apicomplexans B.microti (GreenwichYale_Lab_strain_1 2016) https://genome.ucsc.edu/h/GCA_001650075.1 @@ -389,6 +429,7 @@ Cryptococcus neoformans var. grubii H99 2018 INSDC GCA_003011985.1 no 0 14 0 Cry Cryptococcus neoformans var. grubii KN99 GenBank GCA_002216725.1 no 0 0 14 Cryptococcus neoformans var. grubii KN99 FungiDB 178876.0 GCA_002216725.1_ASM221672v1 GCA_002216725.1 False Cryptococcus neoformans var. grubii basidiomycetes C.neoformans var. grubii (KN99 2017) https://genome.ucsc.edu/h/GCA_002216725.1 Cryptococcus neoformans strain:VNII INSDC GCA_022832995.1 no 0 0 14 Cryptococcus neoformans strain:VNII FungiDB 5207.0 GCA_022832995.1_ASM2283299v1 GCA_022832995.1 False Cryptococcus neoformans basidiomycetes C.neoformans (VNII 2022) https://genome.ucsc.edu/h/GCA_022832995.1 Cryptosporidium parvum 2022 INSDC GCA_019844115.2 no 0 0 8 Cryptosporidium parvum 2022 CryptoDB 5807.0 GCA_019844115.2_ASM1984411v2 GCA_019844115.2 False Cryptosporidium parvum apicomplexans C.parvum (2021) https://genome.ucsc.edu/h/GCA_019844115.2 +Cryptosporidium parvum IOWA-ATCC GenBank GCA_015245375.1 no 0 0 8 Cryptosporidium parvum IOWA-ATCC CryptoDB 5807.0 GCA_015245375.1_ASM1524537v1 GCA_015245375.1 False Cryptosporidium parvum apicomplexans C.parvum (IOWA-ATCC 2020) https://genome.ucsc.edu/h/GCA_015245375.1 Cavia porcellus 2N INSDC GCA_000151735.1 yes 0 3143 0 Cavia porcellus 2N HostDB 10141.0 GCF_000151735.1_Cavpor3.0 GCA_000151735.1 GCF_000151735.1 False Cavia porcellus domestic guinea pig (2N 2008 refseq) https://genome.ucsc.edu/h/GCF_000151735.1 Candida pseudohaemulonii strain B12108 INSDC GCA_003013735.1 yes 0 36 0 [Candida] pseudohaemulonis B12108 FungiDB 418784.0 GCF_003013735.1_Cand_pseudohaemulonii_B12108 GCA_003013735.1 GCF_003013735.1 True Candidozyma pseudohaemuli budding yeast C.pseudohaemulonis https://genome.ucsc.edu/h/GCF_003013735.1 Chrysosporium queenslandicum isolate CBS 280.77 GenBank GCA_001430955.1 yes 2724 0 0 Chrysosporium queenslandicum isolate CBS 280.77 FungiDB 264361.0 GCA_001430955.1_ASM143095v1 GCA_001430955.1 False Chrysosporium queenslandicum ascomycetes C.queenslandicum (CBS 280.77 2015) https://genome.ucsc.edu/h/GCA_001430955.1 @@ -416,10 +457,12 @@ Eimeria falciformis Bayer Haberkorn 1970 GenBank GCA_002271815.1 yes 751 0 0 Eim Encephalitozoon hellem Swiss GenBank GCA_018342045.1 no 0 32 0 Encephalitozoon hellem Swiss MicrosporidiaDB 27973.0 GCA_018342045.1_Swiss_hellem_version_1 GCA_018342045.1 False Encephalitozoon hellem microsporidians E.hellem (Swiss 2021) https://genome.ucsc.edu/h/GCA_018342045.1 Enterocytozoon hepatopenaei EHP-ID16 INSDC GCA_003709115.1 no 0 162 0 Enterocytozoon hepatopenaei EHP-ID16 MicrosporidiaDB 646526.0 GCA_003709115.1_ASM370911v1 GCA_003709115.1 False Ecytonucleospora hepatopenaei microsporidians E.hepatopenaei (EHP-ID16 2018) https://genome.ucsc.edu/h/GCA_003709115.1 Enterocytozoon hepatopenaei strain TH1 GenBank GCA_002081675.1 yes 62 0 0 Enterocytozoon hepatopenaei strain TH1 MicrosporidiaDB 646526.0 GCA_002081675.1_ASM208167v1 GCA_002081675.1 False Ecytonucleospora hepatopenaei microsporidians E.hepatopenaei (TH1 2017) https://genome.ucsc.edu/h/GCA_002081675.1 +Entamoeba histolytica Rahman INSDC GCA_917563895.1 no 0 18523 0 Entamoeba histolytica Rahman AmoebaDB 294381.0 GCA_917563895.1_Assembly_1 GCA_917563895.1 False Entamoeba histolytica HM-1:IMSS E.histolytica HM-1:IMSS (Rahman 2021) https://genome.ucsc.edu/h/GCA_917563895.1 Eimeria maxima Weybridge GenBank GCA_000499605.1 yes 0 3564 0 Eimeria maxima Weybridge ToxoDB 5804.0 GCF_000499605.1_EMW001 GCA_000499605.1 GCF_000499605.1 True Eimeria maxima apicomplexans E.maxima (Weybridge 2013) https://genome.ucsc.edu/h/GCF_000499605.1 Exophiala mesophila strain CBS 40295 GenBank GCA_000836275.1 yes 0 9 0 Exophiala mesophila strain CBS 40295 FungiDB 212818.0 GCF_000836275.1_Exop_meso_CBS40295_V1 GCA_000836275.1 GCF_000836275.1 True Exophiala mesophila ascomycetes E.mesophila https://genome.ucsc.edu/h/GCF_000836275.1 Eimeria mitis Houghton GenBank GCA_000499745.2 yes 0 15978 0 Eimeria mitis Houghton ToxoDB 44415.0 GCF_000499745.2_EMH001 GCA_000499745.2 GCF_000499745.2 True Eimeria mitis apicomplexans E.mitis (Houghton 2013) https://genome.ucsc.edu/h/GCF_000499745.2 Endotrypanum monterogeii strain LV88 GenBank GCA_000333855.2 yes 0 1925 36 Endotrypanum monterogeii strain LV88 TriTrypDB 5705.0 GCA_000333855.2_Endotrypanum_monterogeii-LV88-1.0.3 GCA_000333855.2 False Endotrypanum monterogeii Endotrypanum monterogeii (LV88 2016) https://genome.ucsc.edu/h/GCA_000333855.2 +Entamoeba moshkovskii Laredo GenBank GCA_002914575.1 yes 3460 1147 0 Entamoeba moshkovskii Laredo AmoebaDB 41668.0 GCA_002914575.1_ASM291457v1 GCA_002914575.1 False Entamoeba moshkovskii E.moshkovskii (Laredo 2018) https://genome.ucsc.edu/h/GCA_002914575.1 Eimeria necatrix Houghton GenBank GCA_000499385.1 yes 0 3707 0 Eimeria necatrix Houghton ToxoDB 51315.0 GCF_000499385.1_ENH001 GCA_000499385.1 GCF_000499385.1 True Eimeria necatrix apicomplexans E.necatrix (Houghton 2013) https://genome.ucsc.edu/h/GCF_000499385.1 Exophiala oligosperma strain CBS 72588 GenBank GCA_000835515.1 yes 0 143 0 Exophiala oligosperma strain CBS 72588 FungiDB 215243.0 GCF_000835515.1_Exop_olig_CBS72588_V1 GCA_000835515.1 GCF_000835515.1 True Exophiala oligosperma ascomycetes E.oligosperma https://genome.ucsc.edu/h/GCF_000835515.1 Emergomyces orientalis 5z489 INSDC GCA_002110485.1 yes 0 108 0 Emergomyces orientalis 5z489 FungiDB 1972497.0 GCA_002110485.1_ASM211048v1 GCA_002110485.1 False Emergomyces orientalis ascomycetes E.orientalis (5z489 2017) https://genome.ucsc.edu/h/GCA_002110485.1 @@ -442,12 +485,14 @@ Glossina morsitans Yale INSDC GCA_001077435.1 yes 0 13807 0 Glossina morsitans Y Gregarina niphandrodes Unknown strain GenBank GCA_000223845.4 yes 0 469 0 Gregarina niphandrodes Unknown strain CryptoDB 110365.0 GCF_000223845.1_GNI3 GCA_000223845.4 GCF_000223845.1 True Gregarina niphandrodes apicomplexans G.niphandrodes (2014) https://genome.ucsc.edu/h/GCF_000223845.1 Glossina pallidipes IAEA INSDC GCA_000688715.1 yes 0 1726 0 Glossina pallidipes IAEA VectorBase 7398.0 GCA_000688715.1_Glossina_pallidipes-1.0.3 GCA_000688715.1 False Glossina pallidipes tsetse fly G.pallidipes (2014) https://genome.ucsc.edu/h/GCA_000688715.1 Glossina palpalis IAEA INSDC GCA_000818775.1 yes 0 3926 0 Glossina palpalis IAEA VectorBase 67801.0 GCA_000818775.1_Glossina_palpalis_gambiensis-2.0.1 GCA_000818775.1 False Glossina palpalis gambiensis tsetse fly G.palpalis gambiensis (146720 2015) https://genome.ucsc.edu/h/GCA_000818775.1 +Hyalomma asiaticum Hyas-2018 INSDC GCA_013339685.2 yes 0 6308 11 Hyalomma asiaticum Hyas-2018 VectorBase 266040.0 GCA_013339685.2_BIME_Hyas_1.3 GCA_013339685.2 False Hyalomma asiaticum mite/tick H.asiaticum (Hyas-2018 2020) https://genome.ucsc.edu/h/GCA_013339685.2 Histoplasma capsulatum G184AR INSDC GCA_017607465.1 no 0 11 0 Histoplasma capsulatum G184AR FungiDB 5037.0 GCA_017607465.1_ASM1760746v1 GCA_017607465.1 False Histoplasma capsulatum ascomycetes H.capsulatum (G184AR 2021) https://genome.ucsc.edu/h/GCA_017607465.1 Histoplasma capsulatum WU24 INSDC GCA_017310585.1 no 0 0 7 Histoplasma capsulatum WU24 FungiDB 5037.0 GCA_017310585.1_ASM1731058v1 GCA_017310585.1 False Histoplasma capsulatum ascomycetes H.capsulatum (WU24 2021) https://genome.ucsc.edu/h/GCA_017310585.1 Hepatospora eriocheir strain GB1 GenBank GCA_002087885.1 yes 1300 0 0 Hepatospora eriocheir strain GB1 MicrosporidiaDB 1081669.0 GCA_002087885.1_ASM208788v1 GCA_002087885.1 False Hepatospora eriocheir microsporidians H.eriocheir (GB1 2017) https://genome.ucsc.edu/h/GCA_002087885.1 Hepatospora eriocheir strain canceri GenBank GCA_002087875.1 no 2344 0 0 Hepatospora eriocheir strain canceri MicrosporidiaDB 1081669.0 GCA_002087875.1_ASM208787v1 GCA_002087875.1 False Hepatospora eriocheir microsporidians H.eriocheir (canceri 2017) https://genome.ucsc.edu/h/GCA_002087875.1 Hanseniaspora guilliermondii strain UTAD222 INSDC GCA_900119595.1 yes 0 208 0 Hanseniaspora guilliermondii strain UTAD222 FungiDB 56406.0 GCA_900119595.1_version_1 GCA_900119595.1 False Hanseniaspora guilliermondii budding yeast H.guilliermondii (UTAD222 2016) https://genome.ucsc.edu/h/GCA_900119595.1 Hammondia hammondi strain H.H.34 GenBank GCA_000258005.2 yes 0 14860 0 Hammondia hammondi strain H.H.34 ToxoDB 99158.0 GCF_000258005.1_HHA1_v02 GCA_000258005.2 GCF_000258005.1 True Hammondia hammondi apicomplexans H.hammondi (H.H.34 2014) https://genome.ucsc.edu/h/GCF_000258005.1 +Haemaphysalis longicornis HaeL-2018 INSDC GCA_013339765.2 yes 0 3874 11 Haemaphysalis longicornis HaeL-2018 VectorBase 44386.0 GCA_013339765.2_BIME_HaeL_1.3 GCA_013339765.2 False Haemaphysalis longicornis longhorned tick (HaeL-2018 2020) https://genome.ucsc.edu/h/GCA_013339765.2 Hamiltosporidium magnivora BE-OM-2 INSDC GCA_004325065.1 yes 0 3550 0 Hamiltosporidium magnivora BE-OM-2 MicrosporidiaDB 148818.0 GCA_004325065.1_BEOM2_v1 GCA_004325065.1 False Hamiltosporidium magnivora microsporidians H.magnivora (BE-OM-2 2019) https://genome.ucsc.edu/h/GCA_004325065.1 Hamiltosporidium magnivora IL-BN-2 INSDC GCA_004325035.1 no 0 3833 0 Hamiltosporidium magnivora IL-BN-2 MicrosporidiaDB 148818.0 GCA_004325035.1_ASM432503v1 GCA_004325035.1 False Hamiltosporidium magnivora microsporidians H.magnivora (IL-BN-2 2019) https://genome.ucsc.edu/h/GCA_004325035.1 Hepatocystis sp. ex Piliocolobus tephrosceles 2019 INSDC GCA_902459845.2 yes 0 2439 0 Hepatocystis sp. ex Piliocolobus tephrosceles 2019 PlasmoDB 2600580.0 GCA_902459845.2_HEP1 GCA_902459845.2 False Hepatocystis sp. ex Piliocolobus tephrosceles apicomplexans H.sp. ex Piliocolobus tephrosceles (2020) https://genome.ucsc.edu/h/GCA_902459845.2 @@ -456,6 +501,7 @@ Hamiltosporidium tvaerminnensis FI-OER-3-3 INSDC GCA_004325045.1 yes 0 2915 0 Ha Hamiltosporidium tvaerminnensis IL-G-3 INSDC GCA_004325075.1 no 0 2738 0 Hamiltosporidium tvaerminnensis IL-G-3 MicrosporidiaDB 1176355.0 GCA_004325075.1_ILG3_v1 GCA_004325075.1 False Hamiltosporidium tvaerminnensis microsporidians H.tvaerminnensis (IL-G-3 2019) https://genome.ucsc.edu/h/GCA_004325075.1 Hanseniaspora uvarum strain AWRI3580 INSDC GCA_001747055.1 yes 0 18 0 Hanseniaspora uvarum strain AWRI3580 FungiDB 29833.0 GCA_001747055.1_ASM174705v1 GCA_001747055.1 False Hanseniaspora uvarum budding yeast H.uvarum (AWRI3580 2016) https://genome.ucsc.edu/h/GCA_001747055.1 Hemileia vastatrix Race XXXIII INSDC GCA_004125335.1 yes 0 116756 0 Hemileia vastatrix Race XXXIII FungiDB 203904.0 GCA_004125335.1_ASM412533v1 GCA_004125335.1 False Hemileia vastatrix coffee rust fungus (Race XXXIII 2019) https://genome.ucsc.edu/h/GCA_004125335.1 +Ixodes persulcatus Iper-2018 INSDC GCA_013358835.2 yes 0 11596 0 Ixodes persulcatus Iper-2018 VectorBase 34615.0 GCA_013358835.2_BIME_Iper_1.3 GCA_013358835.2 False Ixodes persulcatus taiga tick (Iper-2018 2020) https://genome.ucsc.edu/h/GCA_013358835.2 Ixodes ricinus Charles River INSDC GCA_000973045.2 yes 0 204516 0 Ixodes ricinus Charles River VectorBase 34613.0 GCA_000973045.2_ASM97304v2 GCA_000973045.2 False Ixodes ricinus castor bean tick (Charles River 2016) https://genome.ucsc.edu/h/GCA_000973045.2 Ixodes scapularis ISE6 INSDC GCA_002892825.2 no 0 6476 0 Ixodes scapularis ISE6 VectorBase 6945.0 GCF_002892825.2_ISE6_asm2.2_deduplicated GCA_002892825.2 GCF_002892825.2 False Ixodes scapularis black-legged tick (JCVI 2018) https://genome.ucsc.edu/h/GCF_002892825.2 Ixodes scapularis PalLabHiFi INSDC GCF_016920785.2 yes 0 648 0 Ixodes scapularis PalLabHiFi VectorBase 6945.0 GCF_016920785.2_ASM1692078v2 GCA_016920785.2 GCF_016920785.2 True Ixodes scapularis black-legged tick (U.Maryland v2 2021) https://genome.ucsc.edu/h/GCF_016920785.2 @@ -506,6 +552,7 @@ Naegleria fowleri strain ATCC 30894 INSDC GCA_008403515.1 no 0 81 0 Naegleria fo Nakaseomyces glabratus BG2 INSDC GCA_014217725.1 no 0 0 13 Nakaseomyces glabratus BG2 FungiDB 5478.0 GCA_014217725.1_ASM1421772v1 GCA_014217725.1 False Nakaseomyces glabratus budding yeast N.glabratus (BG2 2020) https://genome.ucsc.edu/h/GCA_014217725.1 Nakaseomyces glabratus BG3993 INSDC GCA_020450195.1 no 0 0 13 Nakaseomyces glabratus BG3993 FungiDB 5478.0 GCA_020450195.1_ASM2045019v1 GCA_020450195.1 False Nakaseomyces glabratus budding yeast N.glabratus (BG3993 2021) https://genome.ucsc.edu/h/GCA_020450195.1 Nakaseomyces glabratus CBS138 2020 INSDC GCA_010111755.1 no 0 0 13 Nakaseomyces glabratus CBS138 2020 FungiDB 5478.0 GCF_010111755.1_ASM1011175v1 GCA_010111755.1 GCF_010111755.1 True Nakaseomyces glabratus budding yeast N.glabratus (ATCC 2001 2020) https://genome.ucsc.edu/h/GCF_010111755.1 +Nakaseomyces glabratus DSY562 INSDC GCA_002219185.1 no 0 5 13 Nakaseomyces glabratus DSY562 FungiDB 5478.0 GCA_002219185.1_ASM221918v1 GCA_002219185.1 False Nakaseomyces glabratus budding yeast N.glabratus (DSY562 2017) https://genome.ucsc.edu/h/GCA_002219185.1 Nosema granulosis Ou3-Ou53 INSDC GCA_015832245.1 yes 0 1754 0 Nosema granulosis Ou3-Ou53 MicrosporidiaDB 83296.0 GCA_015832245.1_ASM1583224v1 GCA_015832245.1 False Nosema granulosis microsporidians N.granulosis (Ou3-Ou53 2020) https://genome.ucsc.edu/h/GCA_015832245.1 Naegleria lovaniensis strain ATCC 30569 INSDC GCA_003324165.2 yes 0 109 0 Naegleria lovaniensis strain ATCC 30569 AmoebaDB 51637.0 GCF_003324165.1_Nlova_2.1 GCA_003324165.2 GCF_003324165.1 False Naegleria lovaniensis N.lovaniensis (ATCC 30569 2021) https://genome.ucsc.edu/h/GCF_003324165.1 Nematocida major JUm2507 INSDC GCA_021653875.1 yes 0 111 0 Nematocida major JUm2507 MicrosporidiaDB 1912982.0 GCF_021653875.1_ASM2165387v1 GCA_021653875.1 GCF_021653875.1 True Nematocida major microsporidians N.major (JUm2507 2022) https://genome.ucsc.edu/h/GCF_021653875.1 @@ -554,6 +601,7 @@ Plasmodium ovale curtisi GH01 GenBank GCA_900090035.2 yes 638 0 14 Plasmodium ov Plasmodium ovale wallikeri PowCR01 INSDC GCA_900090025.2 no 0 763 14 Plasmodium ovale wallikeri PowCR01 PlasmoDB 36330.0 GCA_900090025.2_PowCR01 GCA_900090025.2 False Plasmodium ovale malaria parasite P. ovale (2016) https://genome.ucsc.edu/h/GCA_900090025.2 Phlebotomus papatasi Israel INSDC GCA_000262795.1 no 0 106826 0 Phlebotomus papatasi Israel VectorBase 29031.0 GCA_000262795.1_Ppap_1.0 GCA_000262795.1 False Phlebotomus papatasi fly P.papatasi (2012) https://genome.ucsc.edu/h/GCA_000262795.1 Phlebotomus papatasi M1 INSDC GCF_024763615.1 yes 0 640 5 Phlebotomus papatasi M1 VectorBase 29031.0 GCF_024763615.1_Ppap_2.1 GCA_024763615.2 GCF_024763615.1 False Phlebotomus papatasi fly P.papatasi (M1 2022) https://genome.ucsc.edu/h/GCF_024763615.1 +Pyricularia pennisetigena Br36 INSDC GCA_004337985.1 yes 0 103 5 Pyricularia pennisetigena Br36 FungiDB 1578925.0 GCF_004337985.1_PpBr36 GCA_004337985.1 GCF_004337985.1 True Pyricularia pennisetigena ascomycetes P.pennisetigena (Br36 2019 refseq) https://genome.ucsc.edu/h/GCF_004337985.1 Plasmodium praefalciparum strain G01 INSDC GCA_900095595.1 yes 0 39 14 Plasmodium praefalciparum strain G01 PlasmoDB 880534.0 GCA_900095595.1_PPRFG01 GCA_900095595.1 False Plasmodium sp. gorilla clade G1 apicomplexans P.sp. gorilla clade G1 (2018) https://genome.ucsc.edu/h/GCA_900095595.1 Plasmodium reichenowi CDC GenBank GCA_000723685.1 yes 356 0 14 Plasmodium reichenowi CDC PlasmoDB 5854.0 GCF_000723685.1_PREICH001 GCA_000723685.1 GCF_000723685.1 True Plasmodium reichenowi apicomplexans P.reichenowi (CDC 2014) https://genome.ucsc.edu/h/GCF_000723685.1 Plasmodium reichenowi G01 GenBank GCA_900097025.1 no 34 0 14 Plasmodium reichenowi G01 PlasmoDB 5854.0 GCA_900097025.1_PRG01 GCA_900097025.1 False Plasmodium reichenowi apicomplexans P.reichenowi (2018) https://genome.ucsc.edu/h/GCA_900097025.1 @@ -582,6 +630,7 @@ Rhizophagus irregularis A1 (DAOM-664342) GenBank GCA_001593125.1 no 11196 0 0 Rh Rhizophagus irregularis C2 INSDC GCA_020716745.1 no 0 0 33 Rhizophagus irregularis C2 FungiDB 588596.0 GCA_020716745.1_ASM2071674v1 GCA_020716745.1 False Rhizophagus irregularis glomeromycetes (C2 2021) https://genome.ucsc.edu/h/GCA_020716745.1 Raffaelea lauricola RL4 INSDC GCA_014183025.1 yes 0 169 0 Raffaelea lauricola RL4 FungiDB 483707.0 GCA_014183025.1_ASM1418302v1 GCA_014183025.1 False Harringtonia lauricola ascomycetes H.lauricola (RL4 2020) https://genome.ucsc.edu/h/GCA_014183025.1 Rickenella mellea Ricmel1 INSDC GCA_004355085.1 yes 0 848 0 Rickenella mellea Ricmel1 FungiDB 50990.0 GCA_004355085.1_Ricmel1 GCA_004355085.1 False Rickenella mellea basidiomycetes R.mellea (SZMC22713 2019) https://genome.ucsc.edu/h/GCA_004355085.1 +Rhipicephalus microplus Rmic-2018 INSDC GCA_013339725.1 yes 7036 0 11 Rhipicephalus microplus Rmic-2018 VectorBase 6941.0 GCF_013339725.1_ASM1333972v1 GCA_013339725.1 GCF_013339725.1 False Rhipicephalus microplus southern cattle tick (Rmic-2018 2020 refseq) https://genome.ucsc.edu/h/GCF_013339725.1 Rhizopus microsporus var. microsporus ATCC 52814 INSDC GCA_002083745.1 yes 0 560 0 Rhizopus microsporus var. microsporus ATCC 52814 FungiDB 86635.0 GCA_002083745.1_Rhimi_ATCC52814_1 GCA_002083745.1 False Rhizopus microsporus var. microsporus fungi R.microsporus var. microsporus (ATCC 52814 2017) https://genome.ucsc.edu/h/GCA_002083745.1 Rattus norvegicus BN/NHsdMcwi INSDC GCA_015227675.2 yes 0 153 22 Rattus norvegicus BN/NHsdMcwi HostDB 10116.0 GCF_015227675.2_mRatBN7.2 GCA_015227675.2 GCF_015227675.2 True Rattus norvegicus Norway rat BN7.2 https://genome.ucsc.edu/h/GCF_015227675.2 Rhodnius prolixus CDC INSDC GCA_000181055.3 yes 0 16537 0 Rhodnius prolixus CDC VectorBase 13249.0 GCA_000181055.3_Rhodnius_prolixus-3.0.3 GCA_000181055.3 False Rhodnius prolixus bugs R.prolixus (2015) https://genome.ucsc.edu/h/GCA_000181055.3 From 85efa7be4e89945d8085c7ab2b0c3f0c77d0342d Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Sun, 22 Sep 2024 15:57:26 -0700 Subject: [PATCH 2/2] feat: report unmatched assembly ids when building tsv (#89) --- files/build-genomes-files.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/files/build-genomes-files.py b/files/build-genomes-files.py index dabb1f8..87db0a5 100644 --- a/files/build-genomes-files.py +++ b/files/build-genomes-files.py @@ -11,8 +11,8 @@ def get_duplicate_ids(genomes_df): counts = genomes_df["Genome Version/Assembly ID"].value_counts() return list(counts.index.to_series().loc[counts > 1]) -def get_num_unmatched_assemblies(assemblies_df, result_df): - return len(set(assemblies_df["asmId"]) - set(result_df["asmId"])) +def get_unmatched_assemblies(assemblies_df, result_df): + return set(assemblies_df["asmId"]) - set(result_df["asmId"]) def build_genomes_files(): print("Building files") @@ -30,9 +30,9 @@ def build_genomes_files(): result_df = gen_bank_merge_df.combine_first(ref_seq_merge_df).dropna(subset=["ucscBrowser"]) - num_unmatched_assemblies = get_num_unmatched_assemblies(assemblies_df, result_df) - if (num_unmatched_assemblies != 0): - print(f"{num_unmatched_assemblies} assemblies had no matches and are omitted") + unmatched_assemblies = get_unmatched_assemblies(assemblies_df, result_df) + if (len(unmatched_assemblies) != 0): + print(f"Omitted {len(unmatched_assemblies)} assemblies that had no matches: {", ".join(unmatched_assemblies)}") result_df.to_csv(OUTPUT_PATH, index=False, sep="\t")