PCI Genomics

255

Title *

Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collectionuse asterix (*) to get italics

Authors *

Astrid Böhne, Rosa Fernández, Jennifer A. Leonard, Ann M. McCartney, Seanna McTaggart, José Melo-Ferreira, Rita Monteiro, Rebekah A. Oomen, Olga Vinnere Pettersson, Torsten H. StruckPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2024

Picture *

Abstract *

<p>The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA’s pan-European network. To demonstrate the community’s capability and capacity to realise ERGA’s ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA’s member base. SSP aims to aid participating researchers through i) establishing standards for and collecting of sample/ specimen metadata; ii) prioritisation of species for genome sequencing; and iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA’s high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.</p>

Indicate the full web address (DOI or URL) giving public access to these data (if you have any problems with the deposit of your data, please contact contact@genomics.peercommunityin.org). In case all raw data are included in the preprint, indicate the DOI or URL of the preprint. *

https://doi.org/10.1101/2023.06.28.546652You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

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Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@genomics.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint. *

You should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Keywords (optional)

sampling, sample metadata, FAIR and CARE principles, biodiversity genomics, collections

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

ERGA, ERGA BGE, ERGA Pilot, Evolutionary genomics

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

Mara Lawniczak mara@sanger.ac.uk, Tereza Manousaki tereza@hcmr.gr, John Deck jdeck88@gmail.com, Eric Crandell ecrandall@psu.edu, Sophie Mazard smazard@bioplatforms.com, Julian Osuji suggested: Dr. Justin E. Ideozu; justin.ideozu@abbvie.com No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

Opposed reviewers - Suggest up to 5 people not to invite as reviewers. (Optional)

e.g. John Doe [john@doe.com]

Submission date

2023-07-03 10:39:36

Recommender

Francois Sabot

Reviewers

Julian Osuji, Francois Sabot, Anonymous

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