DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering

Gene polymorphism originates from single-nucleotide polymorphisms (SNPs), and the analysis and study of SNPs are of great significance in the field of biogenetics. The haplotype, which consists of the sequence of SNP loci, carries more genetic information than a single SNP. Haplotype assembly plays a significant role in understanding gene function, diagnosing complex diseases, and pinpointing species genes. We propose a novel method, DeepHapNet, for haplotype assembly through the clustering of reads and learning correlations between read pairs. We employ a sequence model called Retentive Network (RetNet), which utilizes a multiscale retention mechanism to extract read features and learn the global relationships among them. Based on the feature representation of reads learned from the RetNet model, the clustering process of reads is implemented using the SpectralNet model, and, finally, haplotypes are constructed based on the read clusters. Experiments with simulated and real datasets show that the method performs well in the haplotype assembly problem of diploid and polyploid based on either long or short reads. The code implementation of DeepHapNet and the processing scripts for experimental data are publicly available at https://github.com/wjj6666/DeepHapNet.