ffq by the Pachter Lab allows retrieval of metadata from SRA, too. I added an example along with GenoMax's where he references. From the paper, it seems it uses NCBI Entrez programming utilities under the hood.
I don't know though if it encounters retrieval limits with the likes of what is being described though.
How to download metadata from SRA database
Hi, I have an issue downloading metadata from the SRA database. My search yields approximately 200,000 results, but when I want to download the metadata for subsequent filtering using SRA run selector, it limits me to a maximum of 40,000 results to download. My question is: how can I download the metadata for all the results that my search returns? Thank you in advance.
1 answer
Here is a specific example of how to use NCBI EntrezDirect utils: different ways of downloading SRA metadata
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You can use NCBI eutils to get the associated runinfo.