A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

Until recently, genome-scale phasing was limited due to the short read sizes of sequence data. Though the use of long-read sequencing can overcome this limitation, they require extensive error correction. The emergence of technologies such as 10X genomics linked read sequencing and Hi-C which uses short-read sequencers along with library preparation protocols that facilitates long-read assemblies have greatly reduced the complexities of genome scale phasing. Moreover, it is possible to accurately assemble phased genome of individual samples using these methods. Therefore, in this study, we compared three phasing strategies which included two sample preparation methods along with the Long Ranger pipeline of 10X genomics and HapCut2 software, namely 10X-LG, 10X-HapCut2, and HiC-HapCut2 and assessed their performance and accuracy. We found that the 10X-LG had the best phasing performance amongst the method analyzed. They had the highest phasing rate (89.6%), longest adjusted N50 (1.24 Mb), and lowest switch error rate (0.07%). Moreover, the phasing accuracy and yield of the 10X-LG stayed over 90% for distances up to 4 Mb and 550 Kb respectively, which were considerably higher than 10X-HapCut2 and Hi-C Hapcut2. The results of this study will serve as a good reference for future benchmarking studies and also for reference-based imputation in Hanwoo.