The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage
Open accessAbstract
Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a 'missing manual' that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.
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Cites
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Versatile and open software for comparing large genomes
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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 · cited 1×
“However, as a result of the cost effectiveness and concomitant popularity of short read technologies, the average quality and contiguity of published genomes has plummeted (36).”
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., Yabana, M., Harada, M., Nagayasu, E., Maruyama, H., et al. (2014) · Genome Research · doi:10.1101/gr.170720.113 · Cited by 1,017
Improving PacBio Long Read Accuracy by Short Read Alignment
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Long-read sequence assembly of the gorilla genome
Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science · doi:10.1126/science.aae0344 · Cited by 333
Cited by
Ashley, E. A. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.86 · Cited by 1,116
The population genetics of structural variants in grapevine domestication
Zhou, Y., Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., & Gaut, B. S. (2019) · Nature Plants · doi:10.1038/s41477-019-0507-8 · Cited by 339
Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits
Chakraborty, M., Emerson, J. J., Macdonald, S. J., & Long, A. D. (2019) · Nature Communications · doi:10.1038/s41467-019-12884-1 · Cited by 186
Self-citationChang, C.-H., & Larracuente, A. M. (2019) · Genetics · doi:10.1534/genetics.118.301765 · Cited by 141
Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk
Kono, N., Nakamura, H., Mori, M., Yoshida, Y., Ohtoshi, R., Malay, A. D., Pedrazzoli Moran, D. A., Tomita, M., Numata, K., & Arakawa, K. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2107065118 · Cited by 99
Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea
Benowitz, K. M., Allan, C. W., Degain, B. A., Li, X., Fabrick, J. A., Tabashnik, B. E., Carrière, Y., & Matzkin, L. M. (2022) · Genetics · doi:10.1093/genetics/iyac037 · Cited by 35
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Metadata
- Authors
- Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., & Emerson, J. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-07-25
- Volume
- 44
- Issue
- 19
- Pages
- gkw654
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2479687279
- Cited by
- 442
- References
- 6
- FWCI
- 10.08
- Type
- journal article
- Language
- en
- Open access
- gold
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