Upgrading to more recent Uniref databases for Humann3

Microbial community profiling HUMAnN
#1

Hi,
Are there any guidelines or things to consider if we want to update the uniref90 database to a more recent version when using humann3 in translated mode? Or should it run smoothly?

#2

I would refer to the custom databases text if you want to build an updated UniRef database for use in translated search:

Off the top of my head, the main things we do with the default UniRef FASTA input is to reduce the sequence header to just the UniRef ID followed by “|” and the sequence’s nucleotide-equivalent length (for RPK normalization). Note that, because UniRef cluster representatives shift over time, the UniRef accessory files (e.g. mappings to other functional annotations) bundled with HUMAnN would likely lose coverage of the updated database.

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#3

@franzosa , Hi, is it possible to get the uniref90 2019 sequence fasta file that is default with Humann3? Thanks!

#4

I think you can export the sequences from the HUMAnN database using the diamond getseq command. We do not host the original file.

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