Question: Best DOI provider for a custom genome index ?
2
gravatar for Charles Plessy
3 months ago by
Charles Plessy2.5k
Japan
Charles Plessy2.5k 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 • 151 views
ADD COMMENTlink modified 3 months ago by d-cameron1.9k • written 3 months ago by Charles Plessy2.5k
2
gravatar for d-cameron
3 months ago by
d-cameron1.9k
Australia
d-cameron1.9k 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 3 months ago • written 3 months ago by d-cameron1.9k
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