Retrieving organism name
Hi,
I usually use the following command to get GCF_id (Accession) from the NCBI. How Can I retrieve the "organism name/source" from NCBI?
cat NZ_id.txt | while read i; do elink -db nuccore -id $i -target assembly|esummary| xtract -pattern DocumentSummary -element AssemblyAccession ; done
Cheers
• 1,334 views
•
link
updated
by
AK
•
written
by
saadleeshehreen
•
written
by
saadleeshehreen
1 answer
Log in to answer this question.
More posts like this
-
Is there a way to make the NCBI entrez or datasets API respect biomial nomenclature within requests?
written by rijan_dhakal •
-
NCBI E-eutilitis not working properly inside a while loop
written by andres.firrincieli
-
Extract NCBI's refseq assembly accession number from nuccore IDs
written by genomes_and_MGEs •
-
Downloading assemblies with description from NCBI with edirect
written by agata •
-
Extracting assembly accession number and protein ID using e-utilities
written by geizetomazetto •
-
more elegant way to bulk download genomes from the NCBI
written by Carambakaracho
-
Using entrez-direct inside a for loop in bash
written by Lille My •
-
How to solve the elink error ?
written by saadleeshehreen
-
Extracting strain name from several assemblies
written by genomes_and_MGEs •
-
Different output fields from efetch
written by Medhat
