Standards recommendations for the Earth BioGenome Project

Mara K. Lawniczak; Richard Durbin; Paul Flicek; Kerstin Lindblad-Toh; Xiaofeng Wei; John M. Archibald; William J. Baker; Katherine Belov; Mark L. Blaxter; Tomas Marques-Bonet; Anna K. Childers; Jonathan A. Coddington; Keith A. Crandall; Andrew J. Crawford; Robert P. Davey; Federica Di Palma; Qi Fang; Wilfried Haerty; Neil Hall; Katherine J. Hoff; Kerstin Howe; Erich D. Jarvis; Warren E. Johnson; Rebecca N. Johnson; Paul J. Kersey; Xin Liu; Jose V. Lopez; Eugene W. Myers; Olga Vinnere Pettersson; Adam M. Phillippy; Monica F. Poelchau; Kim D. Pruitt; Arang Rhie; Juan Carlos Castilla-Rubio; Sunil Kumar Sahu; Nicholas A. Salmon; Pamela S. Soltis; David Swarbreck; Françoise Thibaud-Nissen; Sibo Wang; Jill L. Wegrzyn; Guojie Zhang; He Zhang; Harris A. Lewin; Stephen Richards

doi:10.1073/pnas.2115639118

Standards recommendations for the Earth BioGenome Project

Mara K. Lawniczak
, Richard Durbin
, Paul Flicek
, Kerstin Lindblad-Toh
, Xiaofeng Wei
, John M. Archibald
, William J. Baker
, Katherine Belov
, Mark L. Blaxter
, Tomas Marques-Bonet
, Anna K. Childers
, Jonathan A. Coddington
, Keith A. Crandall
, Andrew J. Crawford
, Robert P. Davey
, Federica Di Palma
, Qi Fang
, Wilfried Haerty
, Neil Hall
, Katherine J. Hoff

Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose V. Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Françoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards

Department of Biological Sciences

Research output: Contribution to journal › Article › peer-review

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.

Original language	American English
Article number	e2115639118
Journal	Proceedings of the National Academy of Sciences (PNAS)
Volume	119
Issue number	4
DOIs	https://doi.org/10.1073/pnas.2115639118
State	Published - Jan 18 2022

Bibliographical note

Funding

DBI:IIBR:CAREER #1943371. This work was supported in part by the US Department of Agriculture, Agricultural Research Service. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The US Department of Agriculture is an equal opportunity provider and employer. The work of K.D.P. and F.T.-N. was supported by the Intramural Research Program of the National Library of Medicine, NIH. K.L.-T. is a distinguished professor funded by the Swedish Research Council. J.A.C. is supported by the Global Genome Initiative of the National Museum of Natural History, Smithsonian Institution. E.D.J. is supported by the Howard Hughes Medical Institute (HHMI). P.F. is supported by Wellcome Grant WT108749/Z/15/Z and the European Molecular Biology Laboratory. J.L.W. is supported by National Science Foundation Grant

Funders	Funder number
National Science Foundation
National Institutes of Health
Howard Hughes Medical Institute
Smithsonian Institution
National Human Genome Research Institute	ZIAHG200398
U.S. National Library of Medicine
National Museum of Natural History
United States Department of Agriculture
Wellcome Trust	WT108749/Z/15/Z
European Molecular Biology Laboratory
Vetenskapsrådet

ASJC Scopus Subject Areas

General

Keywords

Earth BioGenome Project
Ethics
Genome Assembly
Genomics
Genome assembly
Base Sequence/genetics
Humans
Reference Values
Biodiversity
Eukaryota/genetics
Genomics/methods
Sequence Analysis, DNA/methods
Reference Standards
Animals

Disciplines

Biology
Genetics and Genomics

Access to Document

10.1073/pnas.2115639118License: CC BY-NC-ND

Standards recommendations for the Earth BioGenome ProjectFinal published version, 1.39 MBLicense: CC BY

Cite this

Lawniczak, M. K., Durbin, R., Flicek, P., Lindblad-Toh, K., Wei, X., Archibald, J. M., Baker, W. J., Belov, K., Blaxter, M. L., Marques-Bonet, T., Childers, A. K., Coddington, J. A., Crandall, K. A., Crawford, A. J., Davey, R. P., Palma, F. D., Fang, Q., Haerty, W., Hall, N., ... Richards, S. (2022). Standards recommendations for the Earth BioGenome Project. Proceedings of the National Academy of Sciences (PNAS), 119(4), Article e2115639118. https://doi.org/10.1073/pnas.2115639118

Lawniczak, MK, Durbin, R, Flicek, P, Lindblad-Toh, K, Wei, X, Archibald, JM, Baker, WJ, Belov, K, Blaxter, ML, Marques-Bonet, T, Childers, AK, Coddington, JA, Crandall, KA, Crawford, AJ, Davey, RP, Palma, FD, Fang, Q, Haerty, W, Hall, N, Hoff, KJ, Howe, K, Jarvis, ED, Johnson, WE, Johnson, RN, Kersey, PJ, Liu, X, Lopez, JV, Myers, EW, Pettersson, OV, Phillippy, AM, Poelchau, MF, Pruitt, KD, Rhie, A, Castilla-Rubio, JC, Sahu, SK, Salmon, NA, Soltis, PS, Swarbreck, D, Thibaud-Nissen, F, Wang, S, Wegrzyn, JL, Zhang, G, Zhang, H, Lewin, HA & Richards, S 2022, 'Standards recommendations for the Earth BioGenome Project', Proceedings of the National Academy of Sciences (PNAS), vol. 119, no. 4, e2115639118. https://doi.org/10.1073/pnas.2115639118

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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.",

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doi = "10.1073/pnas.2115639118",

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AU - Flicek, Paul

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AU - Wei, Xiaofeng

AU - Archibald, John M.

AU - Baker, William J.

AU - Belov, Katherine

AU - Blaxter, Mark L.

AU - Marques-Bonet, Tomas

AU - Childers, Anna K.

AU - Coddington, Jonathan A.

AU - Crandall, Keith A.

AU - Crawford, Andrew J.

AU - Davey, Robert P.

AU - Palma, Federica Di

AU - Fang, Qi

AU - Haerty, Wilfried

AU - Hall, Neil

AU - Hoff, Katherine J.

AU - Howe, Kerstin

AU - Jarvis, Erich D.

AU - Johnson, Warren E.

AU - Johnson, Rebecca N.

AU - Kersey, Paul J.

AU - Liu, Xin

AU - Lopez, Jose V.

AU - Myers, Eugene W.

AU - Pettersson, Olga Vinnere

AU - Phillippy, Adam M.

AU - Poelchau, Monica F.

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AU - Castilla-Rubio, Juan Carlos

AU - Sahu, Sunil Kumar

AU - Salmon, Nicholas A.

AU - Soltis, Pamela S.

AU - Swarbreck, David

AU - Thibaud-Nissen, Françoise

AU - Wang, Sibo

AU - Wegrzyn, Jill L.

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KW - Eukaryota/genetics

KW - Genomics/methods

KW - Sequence Analysis, DNA/methods

KW - Reference Standards

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Standards recommendations for the Earth BioGenome Project

Abstract

Bibliographical note

Funding

ASJC Scopus Subject Areas

Keywords

Disciplines

Access to Document

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Cite this