NCBI will be phasing out their entrez tools this year, so testing out their new datasets tool as replacement.
So far it's been great. Essentially a more general purpose, officially NCBI backed version of the famous ncbi-genome-download package people are already familiar with.
A quick download of genome accession set is as simple as:
datasets download genome accession --inputfile tmp.acc
Which certainly beats my 31 line script calling on entrez
@naturepoker I missed this news - got an NCBI link?
@kblin as author of https://github.com/kblin/ncbi-genome-download are you in the loop?
@pjacock @kblin I think this was one of the earlier announcements - https://ncbiinsights.ncbi.nlm.nih.gov/2023/10/18/ncbi-datasets-access-sequence-data/
And this page mentions api level entrez will be kept up (but I wouldn't be surprised if it's a slower phase retirement): https://support.nlm.nih.gov/knowledgebase/article/KA-05455/en-us
Effective June 2024, NCBI Datasets will replace legacy Genome and Assembly web resources As part of our ongoing effort to enhance your experience and modernize our services, NCBI will gradually replace the legacy Genome and Assembly resources with the newly introduced NCBI Datasets resource. NCBI Datasets is a continually evolving platform designed to provide easy and intuitive … Continue reading NCBI Datasets: Easily Access and Download Sequence Data and Metadata →
@naturepoker @kblin Ah, to me “In June 2024, NCBI permanently discontinued Entrez Genome and Assembly websites.” sounded much narrower than retirement of the Entrez API and Entrez Direct command line tools wrapping it.
Anyway, glad to hear their new download tools are much improved 👍
naturepoker
Peter Cock
Dr. Kai Blin