I've heard about some groups are using NCBI's RefS...
# taxprofilerm
Michael Panciera
10/21/2025, 5:17 AMI've heard about some groups are using NCBI's RefSeq database as a smaller, faster alternative to the NT database. However, the RefSeq database is actually bigger than NT . . . even if we select down to only the Bacteria + Virus RefSeq databases. Is there some other version of RefSeq that might help--or any other ideas?
j
James Fellows Yates
10/21/2025, 7:55 AMThere is a lot of redundancy and variable quality in RefSeq too - you can do alot of filtering to make it smaller
James Fellows Yates
10/21/2025, 7:55 AMe.g. you probably don't need 18,000 Strep pneumoniae genomes 😬
James Fellows Yates
10/21/2025, 7:56 AMAnd you could remove just contig-level assemblies
James Fellows Yates
10/21/2025, 7:56 AMYou should always explore such databases and not take them on the 'surface'
m
Michael Panciera
10/22/2025, 12:52 AMYes, so I'm wondering if something like this might already exist within the community (I am not qualified to do that kind of filtering and my boss won't have time)
j
James Fellows Yates
10/22/2025, 4:38 AMTo my knowledge no. Taxonomic profiling databases remains to be a bit of a wild west. You can find papers describing more refined ones but often designed for very specific cases
James Fellows Yates
10/22/2025, 4:40 AMBut it's quite easy to Filter refseq, as there are TSV files for each section in RefSeq genome called `asssembly_summary.tsv`of something
James Fellows Yates
10/22/2025, 4:41 AMAnd then there is a assembly status column for example
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