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Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Ryan Lorig-Roach1, Melissa Meredith1, Jean Monlong1
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Biorxiv : the Preprint Server for Biology
|March 3, 2023
Summary
We developed new methods for accurate genome phasing using nanopore data, simplifying and reducing the cost of haplotype resolved de novo assembly. Higher accuracy Oxford Nanopore Technologies reads significantly improve assembly quality.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Haplotype resolved de novo genome assembly is crucial for understanding genetic variation.
- Current methods are often complex and costly, hindering widespread application.
Approach:
- Developed new methods for accurate phasing of nanopore sequencing data using the Shasta genome assembler.
- Introduced GFAse, a modular tool to extend phasing to the chromosome scale.
- Evaluated methods using new Oxford Nanopore Technologies (ONT) PromethION sequencing variants, including proximity ligation data.
Key Points:
- New phasing methods improve accuracy and reduce costs for de novo genome assembly.
- GFAse enables chromosome-scale phasing, a significant advancement.
- Higher accuracy ONT reads, particularly from PromethION, substantially enhance assembly quality.
Conclusions:
- The described methods offer a simplified and more cost-effective approach to haplotype resolved de novo assembly.
- Advancements in nanopore sequencing technology directly translate to improved genome assembly outcomes.
