Journal article

nplnv: accurate detection and genotyping of inversions using long read sub-alignment

Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Duc Cao Minh, Clive J Hoggart, Lachlan JM Coin

BMC BIOINFORMATICS | BMC | Published : 2018

Abstract

BACKGROUND: Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored. RESULT: We present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We benchmark npInv with other tools in both simulation and real data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR les..

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University of Melbourne Researchers

Grants

Awarded by Australian Research Council Future Fellowship


Awarded by Australian Research Council


Funding Acknowledgements

L. C. was supported by an Australian Research Council Future Fellowship during this project (FT110100972). The research is supported by funding from the Australian Research Council (DP140103164). H. S. is funded by a University of Queensland scholarship.