Merge pull request #67 from genomehubs/develop

Add CGP page

static/projects.md

@@ -32,6 +32,8 @@ GoaT hosts dedicated pages for the [Earth Biogenome Project](https://www.earthbi
 
 - [CFGP - Cartilaginous Fish Genome Project](/projects/CFGP)
 
+- [CGP - Cetacean Genomes Project (PRJNA1020146)](/projects/CGP)
+
 - DNA Zoo (in progress)
 
 - [DTOL - Darwin Tree of Life (PRJEB40665)](/projects/DTOL)

static/projects/cgp.md

@@ -0,0 +1,184 @@
+:::grid{container direction="row" spacing="1"}
+::grid[![GoaT](/static/images/CGP.png)]{item xs=3}
+:::
+
+# Cetacean Genomes Project  (CGP)
+
+**GoaT Search Term:** CGP
+
+::grid[**Cetacean Genomes Project** aim is to facilitate generation of reference genomes of all cetacean species. For more information reach the contact info below or access CGP [main project page](https://www.fisheries.noaa.gov/international/science-data/cetacean-genomes-project).]{item xs=8}
+
+**Bioproject ID** PRJNA1020146
+
+**Main Contact**: [Phil Morin]([email protected]), Southwest Fisheries Science Center (NOAA Federal), USA
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+# Summary Data
+
+## CGP Long List
+
+CGP long_list correspond to the subset of species declared as targets by the project. To retrieve the list use the search terms:
+
+- long_list=CGP
+- tax_rank(species)
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+::include{pageId=/projects/reports/target_tree.md project=CGP bioproject=PRJNA1020146 .inline}
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+## CGP Progress Reports
+
+::include{pageId=/projects/reports/progress_by_rank.md project=CGP bioproject=PRJNA1020146 .inline}
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+::include{pageId=/projects/reports/progress_arcs.md project=CGP .inline}
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+::include{pageId=/projects/reports/progress_histo.md project=CGP bioproject=PRJNA1020146 .inline}
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+::include{pageId=/projects/reports/duplication.md project=CGP bioproject=PRJNA1020146 .inline}
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+# CGP Custom Reports
+
+::include{pageId=/projects/reports/target_tree_simple_species.md project=CGP .inline}
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+## Contiguity assessment of Public Cetacean Genomes
+:::grid{container direction="row" spacing="1"}
+
+```report
+report: "scatter"
+result: "assembly"
+x: "contig_n50 AND tax_tree(Cetacea)"
+xField: "contig_n50"
+y: "scaffold_n50 AND tax_tree(Cetacea)"
+cat: "assembly_type=haploid@primary-haploid"
+includeEstimates: false
+xOpts: "10000,1000000000,11,log10"
+yOpts: "10000,1000000000,11,log10"
+highlightArea: "1000000,10000000,1000000000,1000000000,EBP metric zone"
+plotRatio: "auto"
+pointSize: "5"
+scatterThreshold: "10000"
+caption: "Contiguity by assembly type"
+item: true
+xs: 6
+```
+
+
+```report
+report: "scatter"
+result: "assembly"
+x: "contig_n50 AND tax_tree(Cetacea)"
+xField: "contig_n50"
+y: "scaffold_n50 AND tax_tree(Cetacea)"
+cat: "assembly_level=contig,scaffold,chromosome"
+includeEstimates: false
+xOpts: "10000,1000000000,11,log10"
+yOpts: "10000,1000000000,11,log10"
+highlightArea: "1000000,10000000,1000000000,1000000000,EBP metric zone"
+plotRatio: "auto"
+pointSize: "5"
+scatterThreshold: "10000"
+caption: "Contiguity by assembly level"
+item: true
+xs: 6
+```
+:::
+## Completeness Assessment of Public Cetacean Genomes
+:::grid{container direction="row" spacing="1"}
+
+```report
+report: "scatter"
+result: "assembly"
+x: "busco_completeness AND tax_tree(Cetacea)"
+xField: "busco_completeness"
+y: "gene_count AND tax_tree(Cetacea)"
+cat: "assembly_type=haploid@primary-haploid"
+includeEstimates: false
+xOpts: "0,100,,"
+yOpts: ",,,linear"
+plotRatio: "auto"
+pointSize: "5"
+scatterThreshold: "10000"
+caption: "Completeness by assembly type"
+item: true
+xs: 6
+```
+
+
+```report
+report: "scatter"
+result: "assembly"
+x: "busco_completeness AND tax_tree(Cetacea)"
+xField: "busco_completeness"
+y: "gene_count AND tax_tree(Cetacea)"
+cat: "assembly_level=contig,scaffold,chromosome"
+includeEstimates: false
+xOpts: "0,100,,"
+yOpts: ",,,linear"
+plotRatio: "auto"
+pointSize: "5"
+scatterThreshold: "10000"
+caption: "Completeness by assembly level"
+item: true
+xs: 6
+```
+:::
+## Metrics of Public Cetacean Genomes
+:::grid{container direction="row" spacing="1"}
+
+```report
+report: histogram
+x: qv_score and tax_tree(Cetacea) AND tax_rank(species)
+cat: family[10]+
+includeEstimates: false
+xOpts: 20,80,10
+stacked: true
+pointSize: 20
+result: assembly
+taxonomy: ncbi
+caption: "Distribution of QV scores by family"
+item: true
+xs: 6
+```
+
+
+```report
+report: histogram
+x: assembly_span and assembly_type=!alternate-pseudohaplotype and tax_tree(Cetacea) AND tax_rank(species)
+cat: family[12]+
+includeEstimates: false
+stacked: true
+pointSize: 20
+result: assembly
+taxonomy: ncbi
+caption: "Distribution of assembly_span by family"
+item: true
+xs: 6
+```
+:::
+::include{pageId=/projects/reports/contiguity_scatters.md project=CGP bioproject=PRJNA1020146 .inline}
+
+:::grid{container direction="row" spacing="1" class="padded"}
+:::
+
+[back to projects](/projects)

static/projects/reports/target_tree_simple_species.md

@@ -0,0 +1,23 @@
+## Tree representing the declared target list of {{project}}, highlighting species with available assemblies (green)
+
+:::grid{container direction="row" spacing="1" item xs=12}
+
+```report
+report: tree
+x: "tax_tree(Eukaryota) AND long_list={{project}} AND tax_rank(species)"
+y: "assembly_span"
+treeStyle: "rect"
+taxonomy: "ncbi"
+levels: "subspecies,species,genus,family,order,class,phylum"
+includeEstimates: true
+ratio: 3.5
+disableModal: true
+collapseMonotypic: true
+yOpts: "10000000,7000000000,,linear"
+treeThreshold: 10000
+caption: "**Taxa in the declared target list of the {{project}} project.** Orange highlights represent clades with at least one genome available on sequence repositories. Bars = assembly span. Tap tree nodes to browse taxa or long-press to search."
+item: true
+xs: 12
+```
+
+:::