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Updated: Jun 29, 2025
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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
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Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing
Mir Henglin1,2, Maryam Ghareghani3,4, William Harvey5
1Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany.
Biorxiv : the Preprint Server for Biology
|March 26, 2024
Summary
Graphasing generates de novo haplotype-resolved genome assemblies using Strand-seq and assembly graphs. This method achieves high accuracy and contiguity without parental data, outperforming existing techniques.
Area of Science:
- Genomics
- Bioinformatics
- Population Genetics
Background:
- Haplotype information is vital for biomedical and population genetics.
- Current de novo haplotype assembly methods often require parental data or intermediate collapsed assemblies.
Purpose of the Study:
- To present Graphasing, a novel workflow for de novo haplotype-resolved genome assembly.
- To enable chromosome-scale haplotype generation for diploid genomes without parental data.
Main Methods:
- Graphasing synthesizes Strand-seq phase signals with assembly graph topology.
- The workflow integrates with existing assembly pipelines that output assembly graphs and support haplotype assembly.
Main Results:
- Graphasing achieves comparable contiguity, phasing accuracy, and assembly quality to trio-phasing.
- It outperforms Hi-C in phasing accuracy.
- Generates human assemblies with over 18 chromosome-spanning haplotypes.
Conclusions:
- Graphasing provides an efficient and accurate method for de novo haplotype-resolved genome assembly.
- It overcomes limitations of existing strategies, particularly the need for parental data.
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