Genome Project Standards in a New Era of Sequencing
Open accessAbstract
More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.
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The estimated sequence accuracy in the muskox assembly exceeds the recommended value for 'finished genomes'.
“This level of accuracy exceeds the recommend value for “finished genomes”61.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [61]
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The minimum information about a genome sequence (MIGS) specification
Field, D., Garrity, G. M., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T. A., Thomson, N. R., Allen, M. J., Angiuoli, S. V., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1360 · Cited by 1,148 · see citing works
Self-citationThe Sequence Ontology: a tool for the unification of genome annotations
Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., & Ashburner, M. (2005) · Genome Biology · doi:10.1186/gb-2005-6-5-r44 · Cited by 806 · see citing works
Liolios, K., Mavromatis, K., Tavernarakis, N., & Kyrpides, N. C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm884 · Cited by 661 · see citing works
Self-citationAn intermediate grade of finished genomic sequence suitable for comparative analysesPreprint
Blakesley, R. W., Hansen, N. F., Mullikin, J. C., et al. (2004) · Genome Research · doi:10.1101/gr.2648404 · Cited by 74 · see citing works
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Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
Self-citationJolley, K. A., Bray, J. E., & Maiden, M. C. J. (2018) · Wellcome Open Research · doi:10.12688/wellcomeopenres.14826.1 · Cited by 3,551 · see citing works
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882 · see citing works
Self-citationMetaHIT Consortium, Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2939 · Cited by 1,184 · see citing works
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Hungate1000 project collaborators, Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4110 · Cited by 624 · see citing works
Self-citationSun, Z., Harris, H. M. B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I. B., Cooney, J. C., Kagawa, T. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms9322 · Cited by 543 · see citing works
Self-citationBrown, S. D., Nagaraju, S., Utturkar, S., De Tissera, S., Segovia, S., Mitchell, W., Land, M. L., Dassanayake, A., & Köpke, M. (2014) · Biotechnology for Biofuels · doi:10.1186/1754-6834-7-40 · Cited by 145 · see citing works
Genome update: the 1000th genome-a cautionary tale
Lagesen, K., Ussery, D. W., & Wassenaar, T. M. (2010) · Microbiology · doi:10.1099/mic.0.038257-0 · Cited by 62 · see citing works
Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Paton, T., Wintle, R. F., Engstrom, M. D., Gunn, A., & Scherer, S. W. (2024) · Scientific Reports · doi:10.1038/s41598-024-67270-9 · Cited by 4 · see citing works
“This level of accuracy exceeds the recommend value for “finished genomes” 61 .”
Background
- Authors
- Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V., Metha, T., Nelson, K. E., Parkhill, J., Pitluck, S., Qin, X., Read, T. D., Schmutz, J., Sozhamannan, S., Sterk, P., Strausberg, R. L., Sutton, G., Thomson, N. R., Tiedje, J. M., Weinstock, G., Wollam, A., Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, & Detter, J. C.
- Affiliations
- Lawrence Livermore National Laboratory (US)
- Wellcome Sanger Institute (GB)
- Washington University in St. Louis (US)
- Broad Institute (US)
- J. Craig Venter Institute (US)
- Baylor College of Medicine (US)
- Ontario Institute for Cancer Research (CA)
- Los Alamos National Laboratory (US)
- Michigan State University (US)
- Natural Environmental Research Council Centre for Ecology and Hydrology.
- Joint Genome Institute (US)
- National Center for Biotechnology Information (US)
- Seattle Children's Hospital (US)
- Lawrence Berkeley National Laboratory (US)
- J. Craig Venter Institute.
- Georgia Research Alliance (US)
- HudsonAlpha Institute for Biotechnology (US)
- Naval Medical Research Command (US)
- Corresponding author
- Chain, P. S. G.
- Grafham, D. V.
- Fulton, R. S.
- FitzGerald, M. G.
- Hostetler, J.
- Muzny, D.
- Harrison, S. H.
- Kodira, C. D.
- Detter, J. C.
- ORCID
- Chain, P. S. G.
- Fulton, R. S.
- FitzGerald, M. G.
- Muzny, D.
- Ali, J.
- Birren, B.
- Cole, J. R.
- Ding, Y.
- Dugan, S.
- Garrity, G. M.
- Gibbs, R.
- Han, C. S.
- Harrison, S. H.
- Highlander, S.
- Hugenholtz, P.
- Kyrpides, N. C.
- Lapidus, A.
- Malfatti, S. A.
- Parkhill, J.
- Qin, X.
- Read, T. D.
- Schmutz, J.
- Sozhamannan, S.
- Sterk, P.
- Sutton, G.
- Thomson, N. R.
- Tiedje, J. M.
- Weinstock, G.
- Venue
- Science
- Published
- 2009-10-09
- Volume
- 326
- Issue
- 5950
- Pages
- 236-237
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3854948
- OpenAlex
- W2080347313
- Cited by
- 400
- References
- 4
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 10 · 2023: 9 · 2022: 6 · 2021: 9 · 2020: 12 · 2019: 17 · 2018: 20 · 2017: 28 · 2016: 37 · 2015: 37 · 2014: 42 · 2013: 43 · 2012: 44
- FWCI
- 16.37
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- Natural Environment Research Council (NE/D01252X/1)
- National Human Genome Research Institute (U54HG004968, U54HG004973)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- sequencing technologies, data quality assessment
- MeSH terms
- Genome, Sequence Analysis, DNA, Computational Biology, Genomics, Databases, Nucleic Acid
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