How to get a strain name if I know only an assembly ID?

Question

[little_more]

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.

[GenoMax]

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.

Answer 1

[vkkodali_ncbi]

You can try something like this using Entrez Direct (https://www.ncbi.nlm.nih.gov/books/NBK179288/)

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.