I am preparing a custom genome index (for sequence alignment), that combines hg38 plus other reference sequences subjected to more frequent updates (HPV and mycoplasma genomes, mostly updated by addition of new ones).
I intend to use it in a publication and I would like to keep a precise description of what it contains and how I retrieved the data, so I was wondering about putting this information in a repository that provides a DOI. Or since a few Gib are not that big in our days, maybe I can just upload the FASTA file and a README to Zenodo or an equivalent place...
Is there a standard practice in the field, even emerging ?
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written
by
Charles Plessy
1 answer
ENA has a reference registration service for these sort of things. It's even easier if all of your contigs are existing reference contigs (ie you just added/reordered and didn't edit any of the sequence). A SAM header file in the supplementary materials is, in conjunction with a service such as https://www.ebi.ac.uk/ena/software/cram-reference-registry, sufficient for reconstruction of your custom genome.
Edit: you should definitely mention in your paper that that is how you intend for people to rehydrate your genome. Not many people know about such services yet.
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