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. 2022 Jan 25;119(4):e2115639118.
doi: 10.1073/pnas.2115639118.

Standards recommendations for the Earth BioGenome Project

Mara K N Lawniczak  1 , Richard Durbin  1   2 , Paul Flicek  1   3 , Kerstin Lindblad-Toh  4   5 , Xiaofeng Wei  6 , John M Archibald  7 , William J Baker  8 , Katherine Belov  9 , Mark L Blaxter  1 , Tomas Marques Bonet  10   11   12   13 , Anna K Childers  14 , Jonathan A Coddington  15 , Keith A Crandall  16 , Andrew J Crawford  17 , Robert P Davey  18 , Federica Di Palma  19 , Qi Fang  20 , Wilfried Haerty  21 , Neil Hall  19   21 , Katharina J Hoff  22 , Kerstin Howe  1 , Erich D Jarvis  23   24 , Warren E Johnson  25   26 , Rebecca N Johnson  15 , Paul J Kersey  27 , Xin Liu  6 , Jose Victor Lopez  28 , Eugene W Myers  29 , Olga Vinnere Pettersson  30 , Adam M Phillippy  31 , Monica F Poelchau  32 , Kim D Pruitt  33 , Arang Rhie  31 , Juan Carlos Castilla-Rubio  34 , Sunil Kumar Sahu  6   20 , Nicholas A Salmon  1 , Pamela S Soltis  35 , David Swarbreck  21 , Françoise Thibaud-Nissen  33 , Sibo Wang  6 , Jill L Wegrzyn  36   37 , Guojie Zhang  38   39   40   41 , He Zhang  42 , Harris A Lewin  43   44 , Stephen Richards  45
Affiliations

Standards recommendations for the Earth BioGenome Project

Mara K N Lawniczak et al. Proc Natl Acad Sci U S A. .

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Keywords: Earth BioGenome Project; ethics; genome assembly; genomics.

PubMed Disclaimer

Conflict of interest statement

Competing interest statement: P.F. is a member of the scientific advisory boards of Fabric Genomics, Inc. and Eagle Genomics, Ltd.

Figures

Fig. 1.
Fig. 1.
An example of the documentation that should occur as a sample is being processed. The SPECIMEN_ID (the Natural History Museum, London [NHMUK] barcode under the fly) is photographed alongside the specimen and the barcoded tubes into which different samples of that specimen will be placed. The metadata tracking sheet would have three entries for this fly, where collection-related information would be identical, but tissue type and tissue size would vary (e.g., head, thorax, and abdomen, each in a separate tube). Image credit: M.K.N.L.
Fig. 2.
Fig. 2.
Recommended EBP INSDC assembly BioProject submission structure. Alternatives on this theme could include maternal assembly and paternal assembly at the DataBioProject levels, when complete genome assemblies are generated for both haplotypes of a diploid sexually reproducing species. “Your Project” represents a project sequencing multiple genomes, such as the VGP or DToL.
Fig. 3.
Fig. 3.
Recommended future EBP data service portal. Researchers would easily apply for the hardware resources that are shared by the EBP affiliated project networks.
See this image and copyright information in PMC

References

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