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Add CGP page
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:::grid{container direction="row" spacing="1"} | ||
::grid[![GoaT](/static/images/CGP.png)]{item xs=3} | ||
::: | ||
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# Cetacean Genomes Project (CGP) | ||
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**GoaT Search Term:** CGP | ||
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::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} | ||
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**Bioproject ID** PRJNA1020146 | ||
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**Main Contact**: [Phil Morin]([email protected]), Southwest Fisheries Science Center (NOAA Federal), USA | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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# Summary Data | ||
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## CGP Long List | ||
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CGP long_list correspond to the subset of species declared as targets by the project. To retrieve the list use the search terms: | ||
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- long_list=CGP | ||
- tax_rank(species) | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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::include{pageId=/projects/reports/target_tree.md project=CGP bioproject=PRJNA1020146 .inline} | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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## CGP Progress Reports | ||
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::include{pageId=/projects/reports/progress_by_rank.md project=CGP bioproject=PRJNA1020146 .inline} | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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::include{pageId=/projects/reports/progress_arcs.md project=CGP .inline} | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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::include{pageId=/projects/reports/progress_histo.md project=CGP bioproject=PRJNA1020146 .inline} | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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::include{pageId=/projects/reports/duplication.md project=CGP bioproject=PRJNA1020146 .inline} | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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# CGP Custom Reports | ||
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::include{pageId=/projects/reports/target_tree_simple_species.md project=CGP .inline} | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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## Contiguity assessment of Public Cetacean Genomes | ||
:::grid{container direction="row" spacing="1"} | ||
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```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 | ||
``` | ||
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```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"} | ||
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```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 | ||
``` | ||
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```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"} | ||
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```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 | ||
``` | ||
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```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} | ||
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:::grid{container direction="row" spacing="1" class="padded"} | ||
::: | ||
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[back to projects](/projects) |
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## Tree representing the declared target list of {{project}}, highlighting species with available assemblies (green) | ||
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:::grid{container direction="row" spacing="1" item xs=12} | ||
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```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 | ||
``` | ||
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::: |