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Title: Accurate detection of complex structural variations using single molecule sequencing
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  more » « less
Award ID(s):
1732253
NSF-PAR ID:
10058336
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Nature methods
ISSN:
1548-7091
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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