Question: Is there way to get genbank assembly id from nuccore id using ncbi eutils ?
2
gravatar for Prasad
11 months ago by
Prasad 30
United States
Prasad 30 wrote:

Hello,

I am trying to get the assembly id (for eg. GCA_000312685.1 ) for the nuccore id (CP003157.1) using eutils?

For the WGS nuccore id such as CAJY00000000 you can get the the assembly id from assembly_summary_genebank.txt file but I want to get assembly id for ids which are not WGS.

Thanks. Prasad

eutils entrez • 439 views
ADD COMMENTlink modified 11 months ago by genomax78k • written 11 months ago by Prasad 30
1
gravatar for genomax
11 months ago by
genomax78k
United States
genomax78k wrote:

Using Entrezdirect:

$ esearch -db nuccore -query "CP003157.1" | elink -db assembly -target assembly | esummary | xtract -pattern DocumentSummary -element AssemblyAccession
GCF_000312685.1

$ esearch -db nuccore -query "CP003157.1" | elink -db assembly -target assembly | esummary | xtract -pattern DocumentSummary -element Genbank
GCA_000312685.1
ADD COMMENTlink modified 11 months ago • written 11 months ago by genomax78k

Thanks for the quick reply. It works.

but is it possible to get GCA_000312685.1 instead of GCF accession?

ADD REPLYlink written 11 months ago by Prasad 30
1

Absolutely. See the second command above.

ADD REPLYlink written 11 months ago by genomax78k

Thanks again for the quick reply. It was really helpful. :)

ADD REPLYlink modified 11 months ago • written 11 months ago by Prasad 30
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