vgp / vgp.github.io Goto Github PK

The top-level landing page is too plain. Suggest adding a few random species pictures arranged in a grid below the data links, with random species reselected on page reload. Avoid using species without images :)

https://vgp.github.io/genomeark/Haemorhous_mexicanus/

From Francoise Thibaud-Nissen at NCBI:

Hi Adam,
It would be really great if the GenomeArk web pages could show the latest assemblies submitted to ENA or GenBank for each species. There is a pretty simple way to the get the assembly accessions automatically using eutils.
For example, to get the latest assembly for taxid 9244 (Calypte anna) that the VGP sequenced (under the VGP umbrella BioProject):
esearch -db bioproject -q 'PRJNA489243' | elink -db bioproject -target assembly -name bioproject_assembly_all | esummary | xtract -pattern DocumentSummary -if Taxid -equals 9244 -if Synonym -element Organism AssemblyName AssemblyType Taxid -block Synonym -element Genbank | more
Calypte anna (Anna's hummingbird) bCalAnn1_v1.p haploid 9244 GCA_003957555.2
Calypte anna (Anna's hummingbird) bCalAnn1_v1.h alternate-pseudohaplotype 9244 GCA_003957575.1

Or to get a list of all the latest assemblies sequenced by the VGP:
esearch -db bioproject -q 'PRJNA489243' | elink -db bioproject -target assembly -name bioproject_assembly_all |esummary | xtract -pattern DocumentSummary -if Synonym -element Organism AssemblyName AssemblyType -block Synonym -element Genbank
Takifugu rubripes (torafugu) fTakRub1.2 alternate haplotype alternate-pseudohaplotype GCA_901000745.3
Streptopelia turtur (birds) bStrTur1.1 haploid GCA_901699155.1
Takifugu rubripes (torafugu) fTakRub1.2 haploid GCA_901000725.2
Streptopelia turtur (birds) bStrTur1.1 alternate haplotype haploid GCA_901699165.1
Syngnathus acus (greater pipefish) fSynAcu1.1 alternate haplotype haploid GCA_901709685.1
[…]

This is essentially the list that you get if when on https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489243 you click on the Assembly link on the right hand side.

Once you have the GenBank assembly accession:
the URLs to the NCBI Assembly pages is: https://www.ncbi.nlm.nih.gov/assembly/,
and the URLs to the ENA is: https://www.ebi.ac.uk/ena/data/view/

Would that be possible to do?
Thanks,

Françoise