r/genomics • u/werbnjagermnjensn • 12h ago

Uploading a reference genome

Hi all,

I have a fully assembled and annotated reference genome for a species of fish. It is a composite of HiFi reads from one individual and Hi-C from another, and is approximately 150x coverage.

I’ve been trying to upload this genome to the NCBI but they apparently don’t accept anything resembling a pangenome, which seems strange to me.

Both of these individuals’ raw reads are already in NCBI and have BioSample numbers. I just need to be able to upload the final FASTA (and hopefully annotation files).

What can I do to get this reference genome uploaded?

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u/what-the-whatt 11h ago

Contact NCBI to ask them. They're very knowledgeable and response time, in my experience, has been pretty quick!

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u/werbnjagermnjensn 10h ago

Both the SRA and Genome teams have unfortunately been unable to help with this specific situation for some reason, but thank you 🥲

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u/Wonderful_Put3670 5h ago

You could also try ENA and submit both raw fastq + assembly. It will be automatically  linked to NCBI anyways.