The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Accurate detection of complex structural variations using single-molecule sequencing
Open accessAbstract
Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings. NGMLR and Sniffles perform highly accurate alignment and structural variation detection from long-read sequencing data.
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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
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
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×
“Copy number variations are observed as decreases (deletions) or increases (amplifications) in aligned read coverage 12 , and other types of SVs are identified by the arrangement of paired-end reads or split-read alignments 13–16 .”
Mapping copy number variation by population-scale genome sequencing
1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., et al. (2011) · Nature · doi:10.1038/nature09708 · Cited by 1,140
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.25 · Cited by 811 · cited 1×
“With the accuracy established, we next used genuine sequencing of an Arabidopsis thaliana trio (Col-0, CVI and the Col-0 x CVI F1 progeny) 38 and Ashkenazi human trio data set from Genome-in-a-Bottle (GiaB) 39 to assess the recall and Mendelian consistency (Table 1 and Supplementary Notes 4 & 5).”
Cited by
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136
Self-citationNanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841
Self-citationA 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
“In contrast to PBSV and Sniffles, SVIM outputs all calls no matter their quality.”
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Metadata
- Authors
- Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C.
- Venue
- Nature Methods
- Published
- 2018-04-30
- Volume
- 15
- Issue
- 6
- Pages
- 461-468
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2950121474
- Cited by
- 1,654
- References
- 5
- FWCI
- 86.34
- Type
- journal article
- Language
- en
- Open access
- green
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- Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C. (2018). Accurate detection of complex structural variations using single-molecule sequencing. Nature Methods. https://doi.org/10.1038/s41592-018-0001-7
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