How to change GCA_ to NC_ annotations (RefSeq)

Question

[beginner123]

I downloaded the data_summary.tsv file via NCBI Datasets, but I need to change the GCA_ style annotations in the file to NC_ annotations in order to create a RefSeq (NC_) reference list. Is there any way to convert RefSeq Assembly to RefSeq accession number?

[cpad0112]

it would be helpful if you can post what you have downloaded and what you want.

[GenoMax]

GCA accessions are GenBank assemblies where as corresponding GCF accessions (if they exist) would be RefSeq.

One way to convert these would be using EntrezDirect:

$ esearch -db assembly -query GCF_000266945 | elink -target nuccore | efetch -format acc
NC_018026.1
NC_018025.1
CP003361.1
CP003360.1

[Istvan Albert]

looks like we wrote the exact same thing at the same time :-) - just took a detour in investigating the assembly stats

Answer 1

[Istvan Albert]

Interesting question I assumed the assembly summary would have that - turns out it does not. Upon some trial and error it seems you can link this up in the following way using Entrez Direct:

esearch -db assembly -query GCA_009858895 | elink -target nuccore | efetch -format acc

prints:

NC_045512.2
MN908947.3

it shows both the RefSeq and the GenBank entries of the same data.