Question: How to get a strain name if I know only an assembly ID?
0
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
0
gravatar for vkkodali
22 days ago by
vkkodali450
United States
vkkodali450 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 22 days ago by vkkodali450
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1554 users visited in the last hour