Question: Best DOI provider for a custom genome index ?
2
gravatar for Charles Plessy
14 months ago by
Charles Plessy2.7k
Japan
Charles Plessy2.7k wrote:

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 ?

doi metadata genome • 308 views
ADD COMMENTlink modified 14 months ago by d-cameron2.0k • written 14 months ago by Charles Plessy2.7k
2
gravatar for d-cameron
14 months ago by
d-cameron2.0k
Australia
d-cameron2.0k wrote:

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.

ADD COMMENTlink modified 14 months ago • written 14 months ago by d-cameron2.0k
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