Question: How to get a strain name if I know only an assembly ID?
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gravatar for little_more
9 months ago by
little_more10
little_more10 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 • 308 views
ADD COMMENTlink modified 9 months ago by vkkodali1.1k • written 9 months ago by little_more10

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 9 months ago • written 9 months ago by genomax70k
0
gravatar for vkkodali
9 months ago by
vkkodali1.1k
United States
vkkodali1.1k wrote:

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.

ADD COMMENTlink written 9 months ago by vkkodali1.1k
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