Assembly: a resource for assembled genomes at NCBI
Open accessAbstract
The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The number of vertebrate genome assemblies in the NCBI database increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019.
“the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database4 increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019.”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [4]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357 · see citing works
Self-citationThe sheep genome illuminates biology of the rumen and lipid metabolism
Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J. F., Faraut, T., Wu, C., Muzny, D. M., Li, Y., Zhang, W., et al. (2014) · Science · doi:10.1126/science.1252806 · Cited by 514 · see citing works
Flagged first, then by citations
Research works printed but not linked: 20
- [1]van Dijk E.L. Auger H. Jaszczyszyn Y. Thermes C. Ten years of next-generation sequencing technology Trends Genet. 2014 30 418 426 25108476
- [3]Federhen S. Clark K. Barrett T. Parkinson H. Ostell J. Kodama Y. Mashima J. Nakamura Y. Cochrane G. Karsch-Mizrachi I. Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records Stand. Genomic Sci. 2014 9 1275 1277 25197497 PMC4149001
- [4]Barrett T. Clark K. Gevorgyan R. Gorelenkov V. Gribov E. Karsch-Mizrachi I. Kimelman M. Pruitt K.D. Resenchuk S. Tatusova T. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata Nucleic Acids Res. 2012 40 D57 D63 22139929 PMC3245069
- [5]Kollmar M. Kollmar L. Hammesfahr B. Simm D. diArk–the database for eukaryotic genome and transcriptome assemblies in 2014 Nucleic Acids Res. 2015 43 D1107 D1112 25378341 PMC4384042
- [6]Reddy T.B. Thomas A.D. Stamatis D. Bertsch J. Isbandi M. Jansson J. Mallajosyula J. Pagani I. Lobos E.A. Kyrpides N.C. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification Nucleic Acids Res. 2015 43 D1099 D1106 25348402 PMC4384021
- [7]Church D.M. Schneider V.A. Graves T. Auger K. Cunningham F. Bouk N. Chen H.C. Agarwala R. McLaren W.M. Ritchie G.R. Modernizing reference genome assemblies PLoS Biol. 2011 9 e1001091 21750661 PMC3130012
- [8]Kent W.J. Sugnet C.W. Furey T.S. Roskin K.M. Pringle T.H. Zahler A.M. Haussler D. The human genome browser at UCSC Genome Res. 2002 12 996 1006 12045153 PMC186604
- [9]Cunningham F. Amode M.R. Barrell D. Beal K. Billis K. Brent S. Carvalho-Silva D. Clapham P. Coates G. Fitzgerald S. Ensembl 2015 Nucleic Acids Res. 2015 43 D662 D669 25352552 PMC4383879
- [10]Li H. Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 2009 25 1754 1760 19451168 PMC2705234
- [11]Langmead B. Salzberg S.L. Fast gapped-read alignment with Bowtie 2 Nat. Methods 2012 9 357 359 22388286 PMC3322381
- [13]UniProt Consortium UniProt: a hub for protein information Nucleic Acids Res. 2015 43 D204 D212 25348405 PMC4384041
- [14]Kanehisa M. Goto S. Sato Y. Kawashima M. Furumichi M. Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG Nucleic Acids Res. 2014 42 D199 D205 24214961 PMC3965122
- [16]Chen C.H. Kuo T.C. Yang M.H. Chien T.Y. Chu M.J. Huang L.C. Chen C.Y. Lo H.F. Jeng S.T. Chen L.F. Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha BMC Genomics 2014 15 578 25005802 PMC4108785
- [17]Scott J.G. Warren W.C. Beukeboom L.W. Bopp D. Clark A.G. Giers S.D. Hediger M. Jones A.K. Kasai S. Leichter C.A. Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment Genome Biol. 2014 15 466 25315136 PMC4195910
- [18]Chipman A.D. Ferrier D.E. Brena C. Qu J. Hughes D.S. Schroder R. Torres-Oliva M. Znassi N. Jiang H. Almeida F.C. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima PLoS Biol. 2014 12 e1002005 25423365 PMC4244043
- [19]Steinberg K.M. Schneider V.A. Graves-Lindsay T.A. Fulton R.S. Agarwala R. Huddleston J. Shiryev S.A. Morgulis A. Surti U. Warren W.C. Single haplotype assembly of the human genome from a hydatidiform mole Genome Res. 2014 24 2066 2076 25373144 PMC4248323
- [20]Bactrian Camels Genome Sequencing and Analysis Consortium Jirimutu Wang Z. Ding G. Chen G. Sun Y. Sun Z. Zhang H. Wang L. Genome sequences of wild and domestic bactrian camels Nat. Commun. 2012 3 1202 23149746 PMC3514880
- [21]He N. Zhang C. Qi X. Zhao S. Tao Y. Yang G. Lee T.H. Wang X. Cai Q. Li D. Draft genome sequence of the mulberry tree Morus notabilis Nat. Commun. 2013 4 2445 24048436 PMC3791463
- [22]Staats C.C. Kmetzsch L. Schrank A. Vainstein M.H. Fungal zinc metabolism and its connections to virulence Front. Cell. Infect. Microbiol. 2013 3 65 24133658 PMC3796257
- [23]Tan K.K. Tan Y.C. Chang L.Y. Lee K.W. Nore S.S. Yee W.Y. Mat Isa M.N. Jafar F.L. Hoh C.C. AbuBakar S. Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis BMC Genomics 2015 16 93 25888205 PMC4409723
Cited by
Sorted by citations
KEGG for taxonomy-based analysis of pathways and genomes
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M., & Ishiguro-Watanabe, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac963 · Cited by 5,833 · see citing works
Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab776 · Cited by 2,402 · see citing works
A unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367 · see citing works
Schneider, V. A., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H.-C., Kitts, P. A., Murphy, T. D., Pruitt, K. D., Thibaud-Nissen, F., Albracht, D., et al. (2017) · Genome Research · doi:10.1101/gr.213611.116 · Cited by 1,193 · see citing works
Self-citationDatabase Resources of the National Center for Biotechnology Information
Coordinators, N. R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1071 · Cited by 817 · see citing works
Progressive Cactus is a multiple-genome aligner for the thousand-genome era
Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586 · see citing works
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works
The Value of Reference Genomes in the Conservation of Threatened Species
Brandies, P., Peel, E., Hogg, C. J., & Belov, K. (2019) · Genes · doi:10.3390/genes10110846 · Cited by 158 · see citing works
Parsons, C., Stüeken, E. E., Rosen, C. J., Mateos, K., & Anderson, R. E. (2021) · Geobiology · doi:10.1111/gbi.12419 · Cited by 91 · see citing works
Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences
Ruffolo, J. A., Nayfach, S., Gallagher, J., Bhatnagar, A., Beazer, J., Hussain, R., Russ, J., Yip, J., Hill, E., Pacesa, M., et al. (2024) · doi:10.1101/2024.04.22.590591 · Cited by 90 · see citing works
- Authors
- Kitts, P. A., Church, D. M., Thibaud-Nissen, F., Choi, J., Hem, V., Sapojnikov, V., Smith, R. G., Tatusova, T., Xiang, C., Zherikov, A., DiCuccio, M., Murphy, T. D., Pruitt, K. D., & Kimchi, A.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Kitts, Paul A.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-17
- Volume
- 44
- Issue
- D1
- Pages
- D73-D80
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4702866
- OpenAlex
- W2225557190
- Cited by
- 398
- References
- 3
- Citations by year
- 2026: 42 · 2025: 53 · 2024: 68 · 2023: 45 · 2022: 45 · 2021: 52 · 2020: 34 · 2019: 18 · 2018: 18 · 2017: 10 · 2016: 10 · 2015: 2
- FWCI
- 5.26
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (R01CA094025)
- U.S. National Library of Medicine
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- genome assembly, NCBI RefSeq
- MeSH terms
- Animals, Humans, Genome, Internet, Genomics, Databases, Nucleic Acid, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
