-
-
- | CheckM Completeness |
-
-
-
+
+
+
+
+ | CheckM |
+
+
+
+
+
+
+ Completeness:
+
-
-
-
-
- {{ genomeCard.metadata_gene.checkm_completeness.toLocaleString() }}%
-
-
- |
-
-
-
- | CheckM Contamination |
-
-
-
+ Completeness: {{ genomeCard.metadata_gene.checkm_completeness.toLocaleString() }}%
+
+
+ |
+
+
+
+
+
+
+ Contamination:
+
-
-
-
-
- {{ genomeCard.metadata_gene.checkm_contamination.toLocaleString() }}%
-
-
- |
-
+ Contamination: {{ genomeCard.metadata_gene.checkm_contamination.toLocaleString() }}%
+
+
+
+
+
+
+
+
+
+ Strain Heterogeneity:
+
+
+
+ Strain Heterogeneity: {{ genomeCard.metadata_gene.checkm_strain_heterogeneity.toLocaleString() }}
+
+
+ |
+
-
- | CheckM Strain Heterogeneity |
-
-
-
+
+ | CheckM2 |
+
+
+
+
+
+
+ Completeness:
+
-
-
-
-
- {{ genomeCard.metadata_gene.checkm_strain_heterogeneity.toLocaleString() }}
-
-
- |
-
+ Completeness: {{ genomeCard.metadata_gene.checkm2_completeness.toLocaleString() }}%
+
+
+ |
+
+
+
+
+
+
+ Contamination:
+
+
+
+ Contamination: {{ genomeCard.metadata_gene.checkm2_contamination.toLocaleString() }}%
+
+
+ |
+
+
+
+
+
+
+ Model:
+
+
+
+ Model: {{ genomeCard.metadata_gene.checkm2_model }}
+
+
+ |
+
-
- | 5S Count |
-
-
-
+
+
+ | 5S Count |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_gene.lsu_5s_count.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_gene.lsu_5s_count.toLocaleString() }}
+
+
+ |
+
-
- | 16S Count |
-
-
-
+
+ | 16S Count |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_gene.ssu_count.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_gene.ssu_count.toLocaleString() }}
+
+
+ |
+
-
- | 23S Count |
-
-
-
+
+ | 23S Count |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_gene.lsu_23s_count.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_gene.lsu_23s_count.toLocaleString() }}
+
+
+ |
+
-
- | tRNA Count |
-
-
-
+
+ | tRNA Count |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.trna_aa_count.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.trna_aa_count.toLocaleString() }}
+
+
+ |
+
-
- | Contig Count |
-
-
-
+
+ | Contig Count |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.contig_count.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.contig_count.toLocaleString() }}
+
+
+ |
+
-
- | N50 Contigs |
-
-
-
+
+ | N50 Contigs |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.n50_contigs.toLocaleString() }} bp
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.n50_contigs.toLocaleString() }} bp
+
+
+ |
+
-
- | Longest Contig |
-
-
-
+
+ | Longest Contig |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.longest_contig.toLocaleString() }} bp
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.longest_contig.toLocaleString() }} bp
+
+
+ |
+
-
- | Scaffold Count |
-
-
-
+
+ | Scaffold Count |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.scaffold_count.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.scaffold_count.toLocaleString() }}
+
+
+ |
+
-
- | N50 Scaffolds |
-
-
-
+
+ | N50 Scaffolds |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.n50_scaffolds.toLocaleString() }} bp
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.n50_scaffolds.toLocaleString() }} bp
+
+
+ |
+
-
- | Longest Scaffold |
-
-
-
+
+ | Longest Scaffold |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.longest_scaffold.toLocaleString() }} bp
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.longest_scaffold.toLocaleString() }} bp
+
+
+ |
+
-
- | Genome Size |
-
-
-
+
+ | Genome Size |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.genome_size.toLocaleString() }} bp
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.genome_size.toLocaleString() }} bp
+
+
+ |
+
-
- | Protein Count |
-
-
-
+
+ | Protein Count |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_gene.protein_count.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_gene.protein_count.toLocaleString() }}
+
+
+ |
+
-
- | Coding Density |
-
-
-
+
+ | Coding Density |
+
+
+
+
+
+
+
-
-
-
-
- {{ parseFloat(genomeCard.metadata_gene.coding_density).toFixed(2).toLocaleString() }}%
-
-
- |
-
+ {{ parseFloat(genomeCard.metadata_gene.coding_density).toFixed(2).toLocaleString() }}%
+
+
+ |
+
-
- | GC Percentage |
-
-
-
+
+ | GC Percentage |
+
+
+
+
+
+
+
-
-
-
-
- {{ parseFloat(genomeCard.metadata_nucleotide.gc_percentage).toFixed(2).toLocaleString() }}%
-
-
- |
-
+ {{ parseFloat(genomeCard.metadata_nucleotide.gc_percentage).toFixed(2).toLocaleString() }}%
+
+
+ |
+
-
- | Ambiguous Bases |
-
-
-
+
+ | Ambiguous Bases |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadata_nucleotide.ambiguous_bases.toLocaleString() }}
-
-
- |
-
+ {{ genomeCard.metadata_nucleotide.ambiguous_bases.toLocaleString() }}
+
+
+ |
+
-
-
- | GTDB representative |
+
+
+ | GTDB representative |
-
-
-
+
+
+
-
-
-
+ |
+
- {{ genomeCard.speciesRepName }}
-
- |
-
-
-
-
+
- {{ genomeCard.speciesRepName }}
-
- |
-
- |
-
+ {{ genomeCard.speciesRepName }}
+
+
+
+
+
-
- | GTDB representative of species |
-
-
-
+
+ | GTDB representative of species |
+
+
+
+
+
+
+
-
-
-
-
- {{ genomeCard.metadataTaxonomy.gtdb_representative }}
-
-
- |
-
+ {{ genomeCard.metadataTaxonomy.gtdb_representative }}
+
+
+ |
+
-
+ |
diff --git a/components/genome/GenomeTaxonHistory.vue b/components/genome/GenomeTaxonHistory.vue
index baafee4..359d1f7 100644
--- a/components/genome/GenomeTaxonHistory.vue
+++ b/components/genome/GenomeTaxonHistory.vue
@@ -177,7 +177,7 @@ export default Vue.extend({
methods: {
// Compute the taxon history URL for the current taxon
getHistUrl(taxon: string) {
- return `/taxon-history?from=R80&to=R214&query=${encodeURIComponent(taxon)}`
+ return `/taxon-history?from=R80&to=R220&query=${encodeURIComponent(taxon)}`
},
// Retrieve the taxon history for this accession
diff --git a/components/stats/REDr220.vue b/components/stats/REDr220.vue
new file mode 100644
index 0000000..68d9d43
--- /dev/null
+++ b/components/stats/REDr220.vue
@@ -0,0 +1,56 @@
+
+
+
Bacteria
+
+
+
Archaea
+
+
+
-
+
{{ item.taxonomy.d }}
@@ -53,7 +53,7 @@
|
-
+
{{ item.taxonomy.p }}
@@ -65,7 +65,7 @@
|
-
+
{{ item.taxonomy.c }}
@@ -77,7 +77,7 @@
|
-
+
{{ item.taxonomy.o }}
@@ -89,7 +89,7 @@
|
-
+
{{ item.taxonomy.f }}
@@ -101,7 +101,7 @@
|
-
+
{{ item.taxonomy.g }}
@@ -113,7 +113,7 @@
|
-
+
{{ item.taxonomy.s }}
diff --git a/layouts/default.vue b/layouts/default.vue
index 66ef6ca..7c2196d 100644
--- a/layouts/default.vue
+++ b/layouts/default.vue
@@ -220,6 +220,13 @@ export default {
},
],
navStatistics: [
+ {
+ icon: 'mdi-apps',
+ title: 'Release 220',
+ to: '/stats/r220',
+ nuxt: true,
+ external: false,
+ },
{
icon: 'mdi-apps',
title: 'Release 214',
diff --git a/nuxt.config.js b/nuxt.config.js
index fa2d316..ccb9b47 100644
--- a/nuxt.config.js
+++ b/nuxt.config.js
@@ -63,9 +63,20 @@ export default {
modules: [// https://go.nuxtjs.dev/axios
'@nuxtjs/axios', // https://go.nuxtjs.dev/pwa
'@nuxtjs/pwa', // https://pwa.nuxtjs.org/
- 'cookie-universal-nuxt' // https://www.npmjs.com/package/cookie-universal-nuxt
+ 'cookie-universal-nuxt', // https://www.npmjs.com/package/cookie-universal-nuxt
+ 'nuxt-umami'
],
+ // Umami configuration
+ umami: {
+ autoTrack: true,
+ doNotTrack: false,
+ cache: false,
+ domains: 'gtdb.ecogenomic.org,gtdb-dev.ecogenomic.org',
+ websiteId: process.env.UMAMI_WEBSITE_ID,
+ scriptUrl: 'https://gtdb-stats-test.ecogenomic.org/script.js'
+ },
+
// Axios module configuration: https://go.nuxtjs.dev/config-axios
axios: {
baseUrl: '/'
@@ -153,7 +164,7 @@ export default {
advancedMaxHistory: 50, // Maximum number of history states to retain in advanced search
captchaSiteKey: process.env.CAPTCHA_KEY,
googleAnalyticsId: process.env.GA_TRACKING_ID,
- latestStatsPageUrl: '/stats/r214', // this is used to point to the latest stats page,
+ latestStatsPageUrl: '/stats/r220', // this is used to point to the latest stats page,
nuxtVersion: version,
apiCacheKey: loadApiVersion(),
fastAniJobCookieName: 'fastani-jobs'
diff --git a/package-lock.json b/package-lock.json
index 726bb69..5781ceb 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
{
"name": "gtdb.ecogenomic.org",
- "version": "2.26.1",
+ "version": "2.28.0",
"lockfileVersion": 2,
"requires": true,
"packages": {
"": {
"name": "gtdb.ecogenomic.org",
- "version": "2.26.1",
+ "version": "2.28.0",
"dependencies": {
"@nuxtjs/axios": "^5.13.6",
"@nuxtjs/pwa": "^3.3.5",
@@ -41,6 +41,7 @@
"@types/d3-sankey": "^0.12.3",
"@types/d3v5": "npm:@types/d3@^5.16.4",
"@types/d3v6": "npm:@types/d3@^6.7.5",
+ "nuxt-umami": "^1.2.3",
"semantic-release": "^19.0.2"
}
},
@@ -1734,6 +1735,15 @@
"node": ">=6.9.0"
}
},
+ "node_modules/@babel/standalone": {
+ "version": "7.24.4",
+ "resolved": "https://registry.npmjs.org/@babel/standalone/-/standalone-7.24.4.tgz",
+ "integrity": "sha512-V4uqWeedadiuiCx5P5OHYJZ1PehdMpcBccNCEptKFGPiZIY3FI5f2ClxUl4r5wZ5U+ohcQ+4KW6jX2K6xXzq4Q==",
+ "dev": true,
+ "engines": {
+ "node": ">=6.9.0"
+ }
+ },
"node_modules/@babel/template": {
"version": "7.24.0",
"resolved": "https://registry.npmjs.org/@babel/template/-/template-7.24.0.tgz",
@@ -2857,9 +2867,9 @@
}
},
"node_modules/@jridgewell/sourcemap-codec": {
- "version": "1.4.14",
- "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.14.tgz",
- "integrity": "sha512-XPSJHWmi394fuUuzDnGz1wiKqWfo1yXecHQMRf2l6hztTO+nPru658AyDngaBe7isIxEkRsPR3FZh+s7iVa4Uw=="
+ "version": "1.4.15",
+ "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.15.tgz",
+ "integrity": "sha512-eF2rxCRulEKXHTRiDrDy6erMYWqNw4LPdQ8UQA4huuxaQsVeRPFl2oM8oDGxMFhJUWZf9McpLtJasDDZb/Bpeg=="
},
"node_modules/@jridgewell/trace-mapping": {
"version": "0.3.25",
@@ -3642,6 +3652,142 @@
"node": ">=8"
}
},
+ "node_modules/@nuxt/kit": {
+ "version": "3.11.2",
+ "resolved": "https://registry.npmjs.org/@nuxt/kit/-/kit-3.11.2.tgz",
+ "integrity": "sha512-yiYKP0ZWMW7T3TCmsv4H8+jEsB/nFriRAR8bKoSqSV9bkVYWPE36sf7JDux30dQ91jSlQG6LQkB3vCHYTS2cIg==",
+ "dev": true,
+ "dependencies": {
+ "@nuxt/schema": "3.11.2",
+ "c12": "^1.10.0",
+ "consola": "^3.2.3",
+ "defu": "^6.1.4",
+ "globby": "^14.0.1",
+ "hash-sum": "^2.0.0",
+ "ignore": "^5.3.1",
+ "jiti": "^1.21.0",
+ "knitwork": "^1.1.0",
+ "mlly": "^1.6.1",
+ "pathe": "^1.1.2",
+ "pkg-types": "^1.0.3",
+ "scule": "^1.3.0",
+ "semver": "^7.6.0",
+ "ufo": "^1.5.3",
+ "unctx": "^2.3.1",
+ "unimport": "^3.7.1",
+ "untyped": "^1.4.2"
+ },
+ "engines": {
+ "node": "^14.18.0 || >=16.10.0"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/consola": {
+ "version": "3.2.3",
+ "resolved": "https://registry.npmjs.org/consola/-/consola-3.2.3.tgz",
+ "integrity": "sha512-I5qxpzLv+sJhTVEoLYNcTW+bThDCPsit0vLNKShZx6rLtpilNpmmeTPaeqJb9ZE9dV3DGaeby6Vuhrw38WjeyQ==",
+ "dev": true,
+ "engines": {
+ "node": "^14.18.0 || >=16.10.0"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/defu": {
+ "version": "6.1.4",
+ "resolved": "https://registry.npmjs.org/defu/-/defu-6.1.4.tgz",
+ "integrity": "sha512-mEQCMmwJu317oSz8CwdIOdwf3xMif1ttiM8LTufzc3g6kR+9Pe236twL8j3IYT1F7GfRgGcW6MWxzZjLIkuHIg==",
+ "dev": true
+ },
+ "node_modules/@nuxt/kit/node_modules/globby": {
+ "version": "14.0.1",
+ "resolved": "https://registry.npmjs.org/globby/-/globby-14.0.1.tgz",
+ "integrity": "sha512-jOMLD2Z7MAhyG8aJpNOpmziMOP4rPLcc95oQPKXBazW82z+CEgPFBQvEpRUa1KeIMUJo4Wsm+q6uzO/Q/4BksQ==",
+ "dev": true,
+ "dependencies": {
+ "@sindresorhus/merge-streams": "^2.1.0",
+ "fast-glob": "^3.3.2",
+ "ignore": "^5.2.4",
+ "path-type": "^5.0.0",
+ "slash": "^5.1.0",
+ "unicorn-magic": "^0.1.0"
+ },
+ "engines": {
+ "node": ">=18"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/ignore": {
+ "version": "5.3.1",
+ "resolved": "https://registry.npmjs.org/ignore/-/ignore-5.3.1.tgz",
+ "integrity": "sha512-5Fytz/IraMjqpwfd34ke28PTVMjZjJG2MPn5t7OE4eUCUNf8BAa7b5WUS9/Qvr6mwOQS7Mk6vdsMno5he+T8Xw==",
+ "dev": true,
+ "engines": {
+ "node": ">= 4"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/lru-cache": {
+ "version": "6.0.0",
+ "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-6.0.0.tgz",
+ "integrity": "sha512-Jo6dJ04CmSjuznwJSS3pUeWmd/H0ffTlkXXgwZi+eq1UCmqQwCh+eLsYOYCwY991i2Fah4h1BEMCx4qThGbsiA==",
+ "dev": true,
+ "dependencies": {
+ "yallist": "^4.0.0"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/path-type": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/path-type/-/path-type-5.0.0.tgz",
+ "integrity": "sha512-5HviZNaZcfqP95rwpv+1HDgUamezbqdSYTyzjTvwtJSnIH+3vnbmWsItli8OFEndS984VT55M3jduxZbX351gg==",
+ "dev": true,
+ "engines": {
+ "node": ">=12"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/scule": {
+ "version": "1.3.0",
+ "resolved": "https://registry.npmjs.org/scule/-/scule-1.3.0.tgz",
+ "integrity": "sha512-6FtHJEvt+pVMIB9IBY+IcCJ6Z5f1iQnytgyfKMhDKgmzYG+TeH/wx1y3l27rshSbLiSanrR9ffZDrEsmjlQF2g==",
+ "dev": true
+ },
+ "node_modules/@nuxt/kit/node_modules/semver": {
+ "version": "7.6.0",
+ "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.0.tgz",
+ "integrity": "sha512-EnwXhrlwXMk9gKu5/flx5sv/an57AkRplG3hTK68W7FRDN+k+OWBj65M7719OkA82XLBxrcX0KSHj+X5COhOVg==",
+ "dev": true,
+ "dependencies": {
+ "lru-cache": "^6.0.0"
+ },
+ "bin": {
+ "semver": "bin/semver.js"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/slash": {
+ "version": "5.1.0",
+ "resolved": "https://registry.npmjs.org/slash/-/slash-5.1.0.tgz",
+ "integrity": "sha512-ZA6oR3T/pEyuqwMgAKT0/hAv8oAXckzbkmR0UkUosQ+Mc4RxGoJkRmwHgHufaenlyAgE1Mxgpdcrf75y6XcnDg==",
+ "dev": true,
+ "engines": {
+ "node": ">=14.16"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
+ },
+ "node_modules/@nuxt/kit/node_modules/yallist": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
+ "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
+ "dev": true
+ },
"node_modules/@nuxt/loading-screen": {
"version": "2.0.4",
"resolved": "https://registry.npmjs.org/@nuxt/loading-screen/-/loading-screen-2.0.4.tgz",
@@ -3743,6 +3889,55 @@
"node": ">=8"
}
},
+ "node_modules/@nuxt/schema": {
+ "version": "3.11.2",
+ "resolved": "https://registry.npmjs.org/@nuxt/schema/-/schema-3.11.2.tgz",
+ "integrity": "sha512-Z0bx7N08itD5edtpkstImLctWMNvxTArsKXzS35ZuqyAyKBPcRjO1CU01slH0ahO30Gg9kbck3/RKNZPwfOjJg==",
+ "dev": true,
+ "dependencies": {
+ "@nuxt/ui-templates": "^1.3.2",
+ "consola": "^3.2.3",
+ "defu": "^6.1.4",
+ "hookable": "^5.5.3",
+ "pathe": "^1.1.2",
+ "pkg-types": "^1.0.3",
+ "scule": "^1.3.0",
+ "std-env": "^3.7.0",
+ "ufo": "^1.5.3",
+ "unimport": "^3.7.1",
+ "untyped": "^1.4.2"
+ },
+ "engines": {
+ "node": "^14.18.0 || >=16.10.0"
+ }
+ },
+ "node_modules/@nuxt/schema/node_modules/consola": {
+ "version": "3.2.3",
+ "resolved": "https://registry.npmjs.org/consola/-/consola-3.2.3.tgz",
+ "integrity": "sha512-I5qxpzLv+sJhTVEoLYNcTW+bThDCPsit0vLNKShZx6rLtpilNpmmeTPaeqJb9ZE9dV3DGaeby6Vuhrw38WjeyQ==",
+ "dev": true,
+ "engines": {
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+ "version": "1.3.0",
+ "resolved": "https://registry.npmjs.org/scule/-/scule-1.3.0.tgz",
+ "integrity": "sha512-6FtHJEvt+pVMIB9IBY+IcCJ6Z5f1iQnytgyfKMhDKgmzYG+TeH/wx1y3l27rshSbLiSanrR9ffZDrEsmjlQF2g==",
+ "dev": true
+ }
+ }
+ },
"upath": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/upath/-/upath-2.0.1.tgz",
@@ -41330,6 +42708,12 @@
}
}
},
+ "webpack-virtual-modules": {
+ "version": "0.6.1",
+ "resolved": "https://registry.npmjs.org/webpack-virtual-modules/-/webpack-virtual-modules-0.6.1.tgz",
+ "integrity": "sha512-poXpCylU7ExuvZK8z+On3kX+S8o/2dQ/SVYueKA0D4WEMXROXgY8Ez50/bQEUmvoSMMrWcrJqCHuhAbsiwg7Dg==",
+ "dev": true
+ },
"webpackbar": {
"version": "6.0.1",
"resolved": "https://registry.npmjs.org/webpackbar/-/webpackbar-6.0.1.tgz",
diff --git a/package.json b/package.json
index 8f194c5..98dd3ec 100644
--- a/package.json
+++ b/package.json
@@ -44,6 +44,7 @@
"@types/d3-sankey": "^0.12.3",
"@types/d3v5": "npm:@types/d3@^5.16.4",
"@types/d3v6": "npm:@types/d3@^6.7.5",
+ "nuxt-umami": "^1.2.3",
"semantic-release": "^19.0.2"
}
}
diff --git a/pages/index.vue b/pages/index.vue
index 6def751..c3d175d 100644
--- a/pages/index.vue
+++ b/pages/index.vue
@@ -8,14 +8,14 @@
-
- *** GTDB Release 214.1 is now available 🎉
+
+ *** GTDB Release 220 is now available 🎉
download files
***
- *** GTDB-Tk has been updated to use the R214 taxonomy from v2.3.0***
+ *** GTDB-Tk has been updated to use the R220 taxonomy from v2.4.0***
+
@@ -129,27 +129,27 @@ export default Vue.extend({
},
data: () => ({
/* Bacterial stats */
- nBacTot: 394932,
- nBacS: 80789,
- nBacG: 19153,
- nBacF: 4264,
- nBacO: 1624,
- nBacC: 488,
- nBacP: 161,
+ nBacTot: 584382,
+ nBacS: 107235,
+ nBacG: 23112,
+ nBacF: 4870,
+ nBacO: 1840,
+ nBacC: 538,
+ nBacP: 175,
/* Archaeal stats */
- nArcTot: 7777,
- nArcS: 4416,
- nArcG: 1586,
- nArcF: 508,
- nArcO: 148,
- nArcC: 60,
- nArcP: 20,
+ nArcTot: 12477,
+ nArcS: 5869,
+ nArcG: 1847,
+ nArcF: 564,
+ nArcO: 166,
+ nArcC: 64,
+ nArcP: 19,
/* Summary stats */
- nGenomes: 402709,
- releaseVer: '08-RS214',
- releaseDate: '28th April 2023',
+ nGenomes: 596859,
+ releaseVer: '09-RS220',
+ releaseDate: '24th April 2024',
}),
})
diff --git a/pages/methods.vue b/pages/methods.vue
index 12174cc..e4b6de9 100644
--- a/pages/methods.vue
+++ b/pages/methods.vue
@@ -67,9 +67,9 @@
- Average nucleotide identity (ANI) and alignment fraction (AF) values were calculated
- with FastANI v1.3
- (Jain et al., 2018).
+ From release 220, Average nucleotide identity (ANI) and alignment fraction (AF) values were calculated
+ with skani v0.2.1
+ (Shaw and Yu, 2023).
diff --git a/pages/stats/r214.vue b/pages/stats/r214.vue
index 1e4ddb0..c9f3de3 100644
--- a/pages/stats/r214.vue
+++ b/pages/stats/r214.vue
@@ -70,7 +70,7 @@
- GTDB R207 is comprised of 394,932 bacterial and 7,777 archaeal genomes organized into 80,789 bacterial and 4,416 archaeal species clusters.
+ GTDB R214 is comprised of 394,932 bacterial and 7,777 archaeal genomes organized into 80,789 bacterial and 4,416 archaeal species clusters.
diff --git a/pages/stats/r220.vue b/pages/stats/r220.vue
new file mode 100644
index 0000000..6f1d9c9
--- /dev/null
+++ b/pages/stats/r220.vue
@@ -0,0 +1,663 @@
+
+
+
+
+
+
+
+
+
+
+ GTDB R220 spans 596,859 genomes organized into 113,104 species clusters.
+
+
+
+
+ |
+
+ |
+
+ Bacteria
+ |
+
+ Archaea
+ |
+
+ Total
+ |
+
+
+
+
+ | Phylum |
+ 175 |
+ 19 |
+ 194 |
+
+
+ | Class |
+ 538 |
+ 64 |
+ 602 |
+
+
+ | Order |
+ 1,840 |
+ 166 |
+ 2,006 |
+
+
+ | Family |
+ 4,870 |
+ 564 |
+ 5,434 |
+
+
+ | Genus |
+ 23,112 |
+ 1,847 |
+ 24,959 |
+
+
+ | Species |
+ 107,235 |
+ 5,869 |
+ 113,104 |
+
+
+
+
+
+
+
+ GTDB R220 is comprised of 584,382 bacterial and 12,477 archaeal genomes organized into 107,235 bacterial and
+ 5,869
+ archaeal species clusters.
+
+
+
+
+ |
+ |
+
+ R04-RS89
+ |
+
+ R05-RS95
+ |
+
+ R06-RS202
+ |
+
+ R07-RS207
+ |
+
+ R08-RS214
+ |
+
+ R09-RS220
+ |
+
+ Growth from R08-RS214 (%)
+ |
+
+
+
+
+ | Bacterial genomes |
+ 143,512 |
+ 191,527 |
+ 254,090 |
+ 311,480 |
+ 394,932 |
+ 584,382 |
+ 47.97 |
+
+
+ | Archaeal genomes |
+ 2,392 |
+ 3,073 |
+ 4,316 |
+ 6,062 |
+ 7,777 |
+ 12,477 |
+ 60.43 |
+
+
+ | Bacterial species clusters |
+ 23,458 |
+ 30,238 |
+ 45,555 |
+ 62,291 |
+ 80,789 |
+ 107,235 |
+ 32.73 |
+
+
+ | Archaeal species clusters |
+ 1,248 |
+ 1,672 |
+ 2,339 |
+ 3,412 |
+ 4,416 |
+ 5,869 |
+ 32.90 |
+
+
+
+
+
+
+
+ GTDB taxa are comprised of isolate genomes, metagenome-assembled genomes (MAGs), and single-amplified genomes
+ (SAGs). The following plot indicates the proportion of taxa at each taxonomic rank comprised exclusively of
+ isolate genomes, exclusively of environmental genomes (i.e. MAGs/SAGs), or both isolate and environmental
+ genomes.
+
+
+
+
+
+ Each GTDB species cluster is represented by a single genome. Genomes assembled from the type strain of the
+ species were selected where possible, though the majority of species clusters are currently assigned only
+ placeholder names. The proportion of representatives which are isolates, MAGs, or SAGs is given for each
+ category.
+
+
+
+
+
+ The quality of the genomes selected as GTDB species representatives is given below.
+ Genome completeness and contamination were estimated using
+ CheckM and are colored based
+ on the MIMAG genome standards.
+
+ In general, representative genomes were restricted to having a quality satisfying completeness - 5*contamination >50,
+ unless a large portion of contamination could be attributed to strain heterogeneity.
+ A few exceptions exist in order to retain well-known species with abnormal CheckM quality estimates, where contamination exceeds 10%.
+
+
+
+
+
+
+ Taxa encompassing the largest number of GTDB species clusters is given for each taxonomic rank.
+
+
+
+
+ |
+ Phylum
+ |
+
+ Class
+ |
+
+ Order
+ |
+
+ Family
+ |
+
+ Genus
+ |
+
+
+
+
+ | Pseudomonadota 27,965 |
+ Gammaproteobacteria 15,356 |
+ Bacteroidales 6,195 |
+ Lachnospiraceae 3,746 |
+ Streptomyces 1,070 |
+
+
+ | Bacillota_A 14,790 |
+ Clostridia 14,724 |
+ Burkholderiales 5,345 |
+ Burkholderiaceae 3,332 |
+ Collinsella 947 |
+
+
+ | Bacteroidota 14,787 |
+ Bacteroidia 13,828 |
+ Oscillospirales 5,282 |
+ Flavobacteriaceae 2,433 |
+ Pelagibacter 912 |
+
+
+ | Actinomycetota 11,737 |
+ Alphaproteobacteria 12,479 |
+ Lachnospirales 4,084 |
+ Rhodobacteraceae 2,000 |
+ Prevotella 799 |
+
+
+ | Patescibacteria 4,581 |
+ Actinomycetes 7,939 |
+ Flavobacteriales 3,746 |
+ Bacteroidaceae 1,694 |
+ Pseudomonas_E 795 |
+
+
+ | Bacillota 3,868 |
+ Bacilli 3,868 |
+ Pseudomonadales 3,153 |
+ Oscillospiraceae 1,540 |
+ Flavobacterium 643 |
+
+
+ | Bacillota_I 2,903 |
+ Bacilli_A 2,903 |
+ Rhizobiales 2,980 |
+ Sphingomonadaceae 1,470 |
+ Streptococcus 567 |
+
+
+ | Chloroflexota 2,749 |
+ Verrucomicrobiae 1,804 |
+ Actinomycetales 2,943 |
+ Acutalibacteraceae 1,440 |
+ Cryptobacteroides 533 |
+
+
+ | Verrucomicrobiota 2,454 |
+ Paceibacteria 1,779 |
+ Enterobacterales 2,454 |
+ UBA660 1,353 |
+ Mycobacterium 475 |
+
+
+ | Planctomycetota 2,339 |
+ Coriobacteriia 1,599 |
+ Mycobacteriales 2,194 |
+ Ruminococcaceae 1,247 |
+ Microbacterium 355 |
+
+
+
+
+
+
+
+ Taxa encompassing the largest number of genomes in the GTDB is given for each taxonomic ranks.
+
+
+
+
+ | Phylum |
+ Class |
+ Order |
+ Family |
+ Genus |
+ Species |
+
+
+
+
+ | Pseudomonadota 214,930 |
+ Gammaproteobacteria 183,508 |
+ Enterobacterales 110,273 |
+ Enterobacteriaceae 95,186 |
+ Escherichia 39,673 |
+ Escherichia coli 38,926 |
+
+
+ | Bacillota 82,709 |
+ Bacilli 82,709 |
+ Bacteroidales 58,934 |
+ Lachnospiraceae 35,105 |
+ Klebsiella 22,500 |
+ Klebsiella pneumoniae 18,499 |
+
+
+ | Bacillota_A 80,317 |
+ Clostridia 80,141 |
+ Lactobacillales 47,490 |
+ Muribaculaceae 24,600 |
+ Staphylococcus 21,291 |
+ Staphylococcus aureus 16,021 |
+
+
+ | Bacteroidota 76,591 |
+ Bacteroidia 74,294 |
+ Lachnospirales 36,149 |
+ Staphylococcaceae 21,933 |
+ Streptococcus 20,045 |
+ Salmonella enterica 15,089 |
+
+
+ | Actinomycetota 44,996 |
+ Actinomycetes 34,611 |
+ Pseudomonadales 33,473 |
+ Streptococcaceae 21,213 |
+ Salmonella 15,373 |
+ Streptococcus pneumoniae 9,133 |
+
+
+ | Campylobacterota 11,105 |
+ Alphaproteobacteria 31,226 |
+ Burkholderiales 24,448 |
+ Pseudomonadaceae 17,078 |
+ Acinetobacter 11,458 |
+ Acinetobacter baumannii 8,536 |
+
+
+ | Bacillota_I 10,514 |
+ Campylobacteria 11,105 |
+ Staphylococcales 22,087 |
+ Burkholderiaceae 15,875 |
+ Mycobacterium 11,275 |
+ Pseudomonas aeruginosa 8,390 |
+
+
+ | Patescibacteria 8,106 |
+ Bacilli_A 10,514 |
+ Oscillospirales 21,952 |
+ Bacteroidaceae 15,545 |
+ Pseudomonas 8,578 |
+ Mycobacterium tuberculosis 7,337 |
+
+
+ | Verrucomicrobiota 6,636 |
+ Verrucomicrobiae 5,429 |
+ Mycobacteriales 16,889 |
+ Mycobacteriaceae 15,323 |
+ Pseudomonas_E 7,438 |
+ Enterococcus_B faecium 3,202 |
+
+
+ | Cyanobacteriota 5,634 |
+ Coriobacteriia 5,065 |
+ Campylobacterales 11,064 |
+ Moraxellaceae 12,327 |
+ Vibrio 6,956 |
+ Enterococcus faecalis 3,044 |
+
+
+
+
+
+
+
+ The following graphs show the relative evolutionary divergence (RED) of taxa at each taxonomic rank from
+ phylum to genus. RED values provide an operational approximation of relative time with extant taxa existing
+ in the present (RED=1), the last common ancestor occurring at a fixed time in the past (RED=0), and internal
+ nodes being linearly interpolated between these values according to lineage-specific rates of evolution. RED
+ intervals for normalizing taxa at taxonomic ranks was operationally defined as the median RED value
+ (indicated by a blue bar) at each rank ±0.1 (indicated by grey bars).
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Bacteria
+
+
+
+
+
+ Archaea
+
+
+
+
+
+
+
+ Comparison of GTDB and NCBI taxonomic assignments across GTDB species representative genomes and all GTDB
+ genomes which have an assigned NCBI taxonomy. For each taxonomic rank, a taxon was classified as being
+ unchanged
+ if its name was identical in both taxonomies, passively changed if the GTDB taxonomy provided name information
+ absent in the NCBI taxonomy, or actively changed if the name was different between the two taxonomies.
+
+
+ Phylum names have been updated to follow the valid publication of 42 names in
+ IJSEM. This has resulted in a large
+ number of active phylum name changes relative to NCBI classifications at the time of this release.
+ NCBI is also
+ adopting
+ these new phyla names.
+
+
+
+
+
+
+
+
+
+ Key genomic statistics for the GTDB species representative genomes and all genomes in the GTDB.
+
+ Genomes
+
+
+
+
+
+ Species
+
+
+
+
+
+
+ This plot shows the breakdown of placeholder versus latinized names for each taxonomic rank.
+
+
+
+
+
+
+ |
+ |
+
+ Bacteria: Latin
+ |
+
+ Bacteria: Placeholder
+ |
+
+ Archaea: Latin
+ |
+
+ Archaea: Placeholder
+ |
+
+ Latin
+ |
+
+ Placeholder
+ |
+
+
+
+
+ | Phylum |
+ 74 (42.29%) |
+ 101 (57.71%) |
+ 15 (78.95%) |
+ 4 (21.05%) |
+ 89 (45.88%) |
+ 105 (54.12%) |
+
+
+ | Class |
+ 160 (29.74%) |
+ 378 (70.26%) |
+ 39 (60.94%) |
+ 25 (39.06%) |
+ 199 (33.06%) |
+ 403 (66.94%) |
+
+
+ | Order |
+ 378 (20.54%) |
+ 1,462 (79.46%) |
+ 72 (43.37%) |
+ 94 (56.63%) |
+ 450 (22.43%) |
+ 1,556 (77.57%) |
+
+
+ | Family |
+ 805 (16.53%) |
+ 4,065 (83.47%) |
+ 108 (19.15%) |
+ 456 (80.85%) |
+ 913 (16.80%) |
+ 4,521 (83.20%) |
+
+
+ | Genus |
+ 3,957 (17.12%) |
+ 19,155 (82.88%) |
+ 260 (14.08%) |
+ 1,587 (85.92%) |
+ 4,217 (16.90%) |
+ 20,742 (83.10%) |
+
+
+ | Species |
+ 16,168 (15.08%) |
+ 91,067 (84.92%) |
+ 678 (11.55%) |
+ 5,191 (88.45%) |
+ 16,846 (14.89%) |
+ 96,258 (85.11%) |
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/pages/taxon-history.vue b/pages/taxon-history.vue
index 94efd20..415d27f 100644
--- a/pages/taxon-history.vue
+++ b/pages/taxon-history.vue
@@ -78,7 +78,7 @@ export default Vue.extend({
// The taxon history search model
search: {
from: TaxonHistoryRelease.R80,
- to: TaxonHistoryRelease.R214,
+ to: TaxonHistoryRelease.R220,
taxon: '',
} as TaxonHistorySearch,
diff --git a/static/_redirects b/static/_redirects
index 31e8867..ef6e8ae 100644
--- a/static/_redirects
+++ b/static/_redirects
@@ -1,5 +1,5 @@
-/stats /stats/r214 301
-/stats/ /stats/r214 301
+/stats /stats/r220 301
+/stats/ /stats/r220 301
/genomes* /genome:splat 301
/taxon_history* /taxon-history:splat 301
/taxsearch* /species:splat 301
|