SRA complete metadata

Question

[bioguy]

Hi,

I'm trying to find an up-to-date database containing all (yep, all) the sra sequencing metadata, from number of reads to taxon id to environment (I know lots will be misannotations, that's a future problem).

I've found some tools/posts that describe resources for this, like sraDB:

https://bioconductor.org/packages/release/bioc/html/SRAdb.html

Or that group that developed mash screen, who at some point were at least able to stream all the sras:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1841-x

But the former appears to be a few years out of date (and has a broken download link for their SQLite db), and I can't figure out the methods for the latter.

Does anybody out there have either some code to generate a summary file of metadata and/or an existing resource?

Thanks!

Answer 1

[GenoMax]

NCBI makes SRA metadata files available here: https://ftp.ncbi.nlm.nih.gov/sra/reports/Metadata/ and a list of data: https://ftp.ncbi.nlm.nih.gov/sra/reports/Datalist/

Data is in XML format.

[bioguy]

Amazing, thank you!