Abstract
Although numerous algorithms have been developed to identify large chromosomal rearrangements (i.e., genomic structural variants, SVs), there remains a dearth of approaches to evaluate their results. This is significant, as the accurate identification of SVs is still an outstanding problem whereby no single algorithm has been shown to be able to achieve high sensitivity and specificity across different classes of SVs. The method introduced in this chapter, VaPoR, is specifically designed to evaluate the accuracy of SV predictions using third-generation long sequences. This method uses a recurrence approach and collects direct evidence from raw reads thus avoiding computationally costly whole genome assembly. This chapter would describe in detail as how to apply this tool onto different data types.
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References
Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12(5):363–376
Brand H et al (2014) Cryptic and complex chromosomal aberrations in early-onset neuropsychiatric disorders. Am J Hum Genet 95(4):454–461
Layer RM et al (2014) LUMPY: a probabilistic framework for structural variant discovery. Genome Biol 15(6):R84
Rausch T et al (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28(18):i333–i339
Zhao X et al (2016) Resolving complex structural genomic rearrangements using a randomized approach. Genome Biol 17(1):126
Chaisson MJP et al (2014) Resolving the complexity of the human genome using single-molecule sequencing. Nature 517(7536):608–611
Pendleton M et al (2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods 12(8):780–786
Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13(5):278–289
Shi L et al (2016) Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun 7:12065
Koren S et al (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30(7):693–700
Huddleston J et al (2016) Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res 27(5):677–685. https://doi.org/10.1101/gr.214007.116
Carvalho AB, Dupim EG, Goldstein G (2016) Improved assembly of noisy long reads by k-mer validation. Genome Res 26(12):1710–1720
Gibbs AJ, McIntyre GA (1970) The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. Eur J Biochem 16(1):1–11
Parikh H et al (2016) svclassify: a method to establish benchmark structural variant calls. BMC Genomics 17:64
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Zhao, X. (2018). Validation of Genomic Structural Variants Through Long Sequencing Technologies. In: Bickhart, D. (eds) Copy Number Variants. Methods in Molecular Biology, vol 1833. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8666-8_15
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DOI: https://doi.org/10.1007/978-1-4939-8666-8_15
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