The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Limitations of next-generation genome sequence assembly
Open accessAbstract
High-throughput sequencing technologies promise to transform the fields of genetics and comparative biology by delivering tens of thousands of genomes in the near future. Although it is feasible to construct de novo genome assemblies in a few months, there has been relatively little attention to what is lost by sole application of short sequence reads. We compared the recent de novo assemblies using the short oligonucleotide analysis package (SOAP), generated from the genomes of a Han Chinese individual and a Yoruban individual, to experimentally validated genomic features. We found that de novo assemblies were 16.2% shorter than the reference genome and that 420.2 megabase pairs of common repeats and 99.1% of validated duplicated sequences were missing from the genome. Consequently, over 2,377 coding exons were completely missing. We conclude that high-quality sequencing approaches must be considered in conjunction with high-throughput sequencing for comparative genomics analyses and studies of genome evolution.
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The genome of the cucumber,Cucumis sativus L
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Personalized copy number and segmental duplication maps using next-generation sequencing
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Cited by
Genome structural variation discovery and genotyping
Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630
Self-citationRepetitive DNA and next-generation sequencing: computational challenges and solutions
Treangen, T. J., & Salzberg, S. L. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3117 · Cited by 1,597
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129
“7 earlier findings that length and identity of SDs play an important role in assembly accuracy (Alkan et al., 2011).”
BackgroundSelf-citationThe genome of melon ( Cucumis melo L.)
Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, G., González, V. M., Hénaff, E., Câmara, F., Cozzuto, L., Lowy, E., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205415109 · Cited by 744
eggNOG v4.0: nested orthology inference across 3686 organisms
Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1253 · Cited by 652
Metadata
- Authors
- Alkan, C., Sajjadian, S., & Eichler, E. E.
- Venue
- Nature Methods
- Published
- 2010-11-21
- Volume
- 8
- Issue
- 1
- Pages
- 61-65
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2061338306
- Cited by
- 733
- References
- 7
- FWCI
- 20.79
- Type
- journal article
- Language
- en
- Open access
- green
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