Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Reference-free genome phasing is crucial for analyzing allele inheritance and DNA variation's phenotypic effects.
• Long-read sequencing and de novo assembly are commonly used for comprehensive genome phasing, especially in complex regions.

Purpose of the Study:

• To develop and present novel, cost-effective methods for accurate genome phasing of Oxford Nanopore Technologies (ONT) sequence data.
• To improve the efficiency and accessibility of genome phasing for large-scale genomic studies.

Main Methods:

• Utilized the Shasta genome assembler for accurate phasing of ONT sequence data.
• Developed GFAse, a modular tool to extend phasing contiguity to the chromosome scale.
• Tested methods with new ONT PromethION sequencing variants, including proximity ligation data.

Main Results:

• Demonstrated accurate genome phasing of ONT data using the described methods.
• Showcased substantial improvements in assembly quality with newer, higher-accuracy ONT reads.
• Validated the effectiveness of the Shasta assembler and GFAse tool for large-scale phasing.

Conclusions:

• The developed methods offer a more accessible and accurate approach to reference-free genome phasing.
• Advancements in ONT sequencing technology significantly enhance the quality of genome assembly and phasing.
• These tools facilitate deeper understanding of genomic variation and its impact on phenotypes.