How do I download all genomes with specific ST type from ncbi

Question

[blur]

Hi,

I want to download all the genomes available in NCBI that are a certain ST (sequence type) for Klebsiella. Does anyone know how to do that? I am using NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) I wrote the ST type I wanted in the search engine, but I don't know how to verify that the sequences that I got are what I was aiming at.

I used: (klebsiella ST258) AND "Klebsiella pneumoniae"[orgn:__txid573]

Thank you in advance,

[Joe]

I'm not sure that ST is a field that NCBI specifically tracks unless it happens to be in the name of the deposit, but I could be wrong.

I think you might be better off going via an ST database like PubMLST or BIGSDB to at least obtain a list of accessions and then feed this to NCBI.

Answer 1

[vkkodali_ncbi]

You can use NCBI Datasets for this. Specifically, go to the Genomes page and search for "Klebsiella pneumoniae". Out of the >43K genomes, you can filter ST258 ones by clicking on the "Filters" tab and searching for "ST258" in the "Search Within Results" to get 80 genomes. This is a permissive search and can be noisy. Separately, I see that there are 3 genomes for the organism "Klebsiella pneumoniae subsp. pneumoniae ST258". May be that's what you want?

[blur]

Thank you, I want as many of the deposited isolates as possible (the 80).