Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall

Area of Science:

• Genomics
• Bioinformatics

Background:

• Long-read sequencing (LRS) advances whole-genome sequencing, enabling phased *de novo* genome assembly and discovery of complex structural variants (SVs).
• Challenges remain in LRS cost, scalability, and platform-specific accuracy, necessitating careful consideration of sequence coverage for variant detection sensitivity.

Approach:

• Comparative analysis of genetic variant calling precision and recall between Oxford Nanopore Technologies (ONT) and PacBio HiFi platforms across various sequence coverages.
• Evaluation of read-based versus genome assembly approaches for variant discovery, focusing on structural variants and indels.

Key Points:

• LRS sensitivity for read-based variant calling plateaus around 12-fold coverage, with both ONT and PacBio HiFi demonstrating good performance for SV detection.
• Genome assembly significantly enhances variant calling precision and recall for SVs and indels, particularly in PacBio HiFi datasets.
• PacBio HiFi generally outperforms ONT in assembly-based variant calling quality, as indicated by F1 scores.

Conclusions:

• Experimental design for LRS should balance cost-effectiveness with the need for comprehensive variant discovery.
• Both ONT and PacBio HiFi are valuable tools for genomic research, with specific strengths depending on the application and desired outcomes.
• Continued technological evolution in LRS promises further improvements in genome sequencing completeness and accuracy.