Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection

Boehne, A.; Fernandez, R.; Leonard, J. A.; McCartney, A. M.; McTaggart, S.; Melo-Ferreira, J.; Monteiro, R.; Oomen, R. A.; Vinnere Pettersson, O.; Struck, T. H.

doi:10.1101/2023.06.28.546652

bioRxiv · 10.1101/2023.06.28.546652

Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection

Boehne, A.·Fernandez, R.·Leonard, J. A.·McCartney, A. M.·McTaggart, S.·Melo-Ferreira, J.·Monteiro, R.·Oomen, R. A.·Vinnere Pettersson, O.·Struck, T. H.

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Abstract

The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europes eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGAs pan- European network. To demonstrate the communitys capability and capacity to realise ERGAs 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 ERGAs 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 ERGAs 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.

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Boehne, A., Fernandez, R., Leonard, J. A., McCartney, A. M., McTaggart, S., Melo-Ferreira, J., Monteiro, R., Oomen, R. A., Vinnere Pettersson, O., Struck, T. H.. 2023-06-30. Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection. https://doi.org/10.1101/2023.06.28.546652

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