Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., Schatz, M. C. (June 2018) Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods, 15 (6). pp. 461-468. ISSN 1548-7091
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Abstract
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.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > computers > computer software |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab School of Biological Sciences > Publications |
| Depositing User: | Matt Covey |
| Date: | June 2018 |
| Date Deposited: | 22 May 2018 16:44 |
| Last Modified: | 03 Oct 2019 16:54 |
| PMCID: | PMC5990442 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/36564 |
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