The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
Open accessAbstract
Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. However, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. Sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossible to assemble. Traditionally, draft genomes were upgraded to "phase 3 finished" status using time-consuming and expensive Sanger-based manual finishing processes. For more facile assembly and automated finishing of draft genomes, we present here an automated approach to finishing using long-reads from the Pacific Biosciences RS (PacBio) platform. Our algorithm and associated software tool, PBJelly, (publicly available at https://sourceforge.net/projects/pb-jelly/) automates the finishing process using long sequence reads in a reference-guided assembly process. PBJelly also provides "lift-over" co-ordinate tables to easily port existing annotations to the upgraded assembly. Using PBJelly and long PacBio reads, we upgraded the draft genome sequences of a simulated Drosophila melanogaster, the version 2 draft Drosophila pseudoobscura, an assembly of the Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the Sooty mangabey. With 24× mapped coverage of PacBio long-reads, we addressed 99% of gaps and were able to close 69% and improve 12% of all gaps in D. pseudoobscura. With 4× mapped coverage of PacBio long-reads we saw reads address 63% of gaps in our budgerigar assembly, of which 32% were closed and 63% improved. With 6.8× mapped coverage of mangabey PacBio long-reads we addressed 97% of gaps and closed 66% of addressed gaps and improved 19%. The accuracy of gap closure was validated by comparison to Sanger sequencing on gaps from the original D. pseudoobscura draft assembly and shown to be dependent on initial reference quality.
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Cites
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Cited by
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,029
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology
Lakhundi, S., & Zhang, K. (2018) · Clinical Microbiology Reviews · doi:10.1128/cmr.00020-18 · Cited by 1,637
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Berlin, K., Koren, S., Chin, C.-S., Drake, J. P., Landolin, J. M., & Phillippy, A. M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3238 · Cited by 934
Metadata
- Authors
- English, A. C., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D. M., Reid, J. G., Worley, K. C., & Gibbs, R. A.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-11-21
- Volume
- 7
- Issue
- 11
- Pages
- e47768
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W1974640383
- Cited by
- 889
- References
- 21
- FWCI
- 13.13
- Type
- journal article
- Language
- en
- Open access
- gold
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- English, A. C., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D. M., Reid, J. G., Worley, K. C., & Gibbs, R. A. (2012). Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology. PLoS ONE. https://doi.org/10.1371/journal.pone.0047768
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