nPhase: an accurate and contiguous phasing method for polyploids

Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer
2021 Genome Biology  
AbstractWhile genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains
more » ... average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.
doi:10.1186/s13059-021-02342-x pmid:33926549 pmcid:PMC8082856 fatcat:b6ihvxi64fglhkp44eh3t6tukm