Question: How to get a strain name if I know only an assembly ID?
gravatar for little_more
22 days ago by
little_more0 wrote:

Suppose I have a tree with assembly IDs of different E.coli strains in it (all from NCBI). Is there any common way to replace each assembly ID with the corresponding strain name? I tried using BioPython (efetch) but it raises an error.

assembly • 128 views
ADD COMMENTlink modified 22 days ago by vkkodali450 • written 22 days ago by little_more0

Always post sample ID's when asking a question like this. Posting your code/actual error is also beneficial if you don't want an alternate answer.

ADD REPLYlink modified 22 days ago • written 22 days ago by genomax58k
gravatar for vkkodali
22 days ago by
United States
vkkodali450 wrote:

You can try something like this using Entrez Direct (

esearch -db assembly -q '854998' | esummary | xtract -pattern DocumentSummary -def "NA" -element Taxid Genbank RefSeq Organism

You can replace the id 854998 (which is a RefSeq assembly ID) with either assembly UID, Genbank assembly ID, or an NCBI assembly accession.

ADD COMMENTlink written 22 days ago by vkkodali450
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