Question: How to get a strain name if I know only an assembly ID?
0
gravatar for little_more
11 weeks 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 • 161 views
ADD COMMENTlink modified 11 weeks ago by vkkodali860 • written 11 weeks 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 11 weeks ago • written 11 weeks ago by genomax60k
0
gravatar for vkkodali
11 weeks ago by
vkkodali860
United States
vkkodali860 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 11 weeks ago by vkkodali860
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: 1675 users visited in the last hour