An application to download all genomes in all databases with given keyword (TaxID or name) in one time ?

Question

[yoan.bouzin]

Hello :)

I coded an application to view, compare, and download the available genomes in different databases and then automatically download them, the user use the taxID of the rank or species, or also the name of the rank or the species).

I don't know if there are in the web a kind of application of software do the same thing. Is there a software that can fetch genomes or proteomes of one or more species, through the various databases known at the present time (NCBI, ENSEMBL, JGI, PATRIC, ...) ?

Thanks you :)

regards

Yoan

[Pierre Lindenbaum]

see How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its Sub Txids?

Answer 1

[ikkymohamud]

the genbank DNA database contains sequences from more than 300,000 species.

Answer 2

[Giovanni M Dall'Olio]

You can get something similar with the AnnotationHub package in Bioconductor https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html