Thoughts on custom humann3 reference databases

And to also offer some reply to the original question, I think creating an entire alternate data ecosystem for HUMAnN would be a big undertaking (it’s a big job for us just to create and maintain the default ones). I would not recommend it as a project to someone who is just getting started in computational analysis. Note that HUMAnN’s data ecosystem involves more than the genome/pangenome files themselves - there are also a lot of important annotation files that go along with the sequence data, and without those you’d have mapping results but they wouldn’t be very interpretable.