PhaseME: Automatic rapid assessment of phasing quality and phasing improvement.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Accurate phasing of genomic variations on the same DNA molecule is crucial for predicting mutation consequences.
• Current haplotype phasing methods lack transparency, making it difficult to assess the accuracy and quality of reconstructed haplotypes.

Purpose of the Study:

• To introduce PhaseME, a versatile method for assessing and improving sample phasing results using linkage data.
• To compare the performance of PhaseME across various sequencing technologies, including PacBio, Oxford Nanopore, 10x Genomics, and Illumina.

Main Methods:

• PhaseME utilizes linkage data to provide insights into phasing quality and correctness.
• The method generates reports and summary plots for visualizing phasing performance.
• Comparative analysis of phasing results from different sequencing platforms was performed.

Main Results:

• PhaseME significantly improves phasing accuracy, reducing the Hamming error rate by an average of 22.4% across five technologies.
• The method effectively reduces long switch errors, with a 54.6% improvement for high-quality consensus reads.
• Phasing quality from 10x Genomics and Oxford Nanopore technologies showed significant improvement with minimal impact on phase block N50 length.

Conclusions:

• PhaseME is a universal tool for evaluating and enhancing haplotype phasing quality and accuracy.
• The method leverages linkage information to improve phasing outcomes.
• PhaseME is freely available, promoting wider adoption in genomic research.