NanoSNP: A progressive and haplotype-aware SNP caller on low coverage Nanopore sequencing data


 
 
 Oxford Nanopore sequencing has great potential and advantages in population-scale studies. Due to the cost of sequencing, the depth of whole-genome sequencing for per individual sample must be small. However, the existing SNP callers are aimed at high-coverage Nanopore sequencing reads. Detecting the SNP variants on low-coverage Nanopore sequencing data is still a challenging problem.
 
 
 
 We developed a novel deep learning-based SNP calling method, NanoSNP, to identify the SNP sites (excluding short indels) based on low-coverage Nanopore sequencing reads. In this method, we design a multi-step, multi-scale and haplotype-aware SNP detection pipeline. First, the pileup model in NanoSNP utilizes the naive pileup feature to predict a subset of SNP sites with a Bi-LSTM network. These SNP sites are phased and used to divide the low-coverage Nanopore reads into different haplotypes. Finally, the long-range haplotype feature and short-range pileup feature are extracted from each haplotype. The haplotype model combines two features and predicts the genotype for the candidate site using a Bi-LSTM network. To evaluate the performance of NanoSNP, we compared NanoSNP with Clair, Clair3, Pepper-DeepVariant, and NanoCaller on the low-coverage (∼16X) Nanopore sequencing reads. We also performed cross-genome testing on six human genomes HG002-HG007, respectively. Comprehensive experiments demonstrate that NanoSNP outperforms Clair, Pepper-DeepVariant and NanoCaller in identifying SNPs on low-coverage Nanopore sequencing data, including the difficult-to-map regions and MHC regions in the human genome. NanoSNP is comparable to Clair3 when the coverage exceeds 16X.
 
 
 
 https://github.com/huangnengCSU/NanoSNP.git
