The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Open accessAbstract
Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.
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Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Self-citationDe novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 3×
“The baseline SOAPdenovo assembly (purple star) represents an assembly of 50× of real 76-bp Illumina paired-end (300 bp) reads from S. cerevisiae S228c.”
MethodStrong association of de novo copy number mutations with autism
Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., et al. (2007) · Science · doi:10.1126/science.1138659 · Cited by 2,795
International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750
Stimulus-transcription coupling in neurons: role of cellular immediate-early genes
Morgan, J. I., & Curran, T. (1989) · Trends in Neurosciences · doi:10.1016/0166-2236(89)90096-9 · Cited by 969 · cited 1×
“Lastly, the published zebra finch and chicken assemblies both contain gaps ~700 bp upstream of ERG1 , a major immediate-early gene that connects external stimuli to transcription in neurons 39,40 .”
BackgroundEvolution at Two Levels: On Genes and Form
Carroll, S. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030245 · Cited by 882
FOXP2 and the role of cortico-basal ganglia circuits in speech and language evolution
Enard, W. (2011) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2011.04.008 · Cited by 149
Cited by
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352
Self-citationNonhybrid, 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
PacBio Sequencing and its Applications
Rhoads, A., & Au, K. F. (2015) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.08.002 · Cited by 2,135
Characterizing and measuring bias in sequence data
Ross, M. G., Russ, C., Costello, M., Hollinger, A., Lennon, N. J., Hegarty, R., Nusbaum, C., & Jaffe, D. B. (2013) · Genome Biology · doi:10.1186/gb-2013-14-5-r51 · Cited by 909
Metadata
- Authors
- Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., & Phillippy, A. M.
- Venue
- Nature Biotechnology
- Published
- 2012-07
- Volume
- 30
- Issue
- 7
- Pages
- 693-700
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2157888653
- Cited by
- 1,011
- References
- 9
- FWCI
- 32.06
- Type
- journal article
- Language
- en
- Open access
- green
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- Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., & Phillippy, A. M. (2012). Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology. https://doi.org/10.1038/nbt.2280
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