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Related Experiment Video

Updated: Aug 23, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

HAT: haplotype assembly tool using short and error-prone long reads.

Ramin Shirali Hossein Zade¹, Aysun Urhan^1,2, Alvaro Assis de Souza¹

¹Delft Bioinformatics Lab, Delft University of Technology Van Mourik, 2628 XE Delft, The Netherlands.

Bioinformatics (Oxford, England)

|October 29, 2022

Summary

This summary is machine-generated.

Haplotype reconstruction from DNA sequencing data is essential for understanding genotype-phenotype associations. The new HAT tool effectively reconstructs haplotypes using both short and long reads, outperforming existing methods.

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Last Updated: Aug 23, 2025

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Area of Science:

Genomics
Bioinformatics

Background:

Haplotypes, the alleles inherited together on a chromosome, are crucial for genotype-phenotype association studies.
Monoploid reference genomes lack haplotype co-occurrence information, limiting their utility.
Existing haplotype reconstruction methods face limitations, especially with low genetic variation between homologous chromosomes.

Purpose of the Study:

To introduce HAT, a novel haplotype assembly tool.
To improve the reconstruction of complete and reliable haplotypes from DNA sequencing data.

Main Methods:

HAT utilizes both short and long DNA sequencing reads.
It integrates these reads with a reference genome for haplotype assembly.
The tool leverages the accuracy of short reads and the length of long reads.

Main Results:

HAT was tested on the aneuploid yeast strain Saccharomyces pastorianus CBS1483.
Performance was evaluated on simulated polyploid datasets of the same strain.
HAT demonstrated superior performance compared to existing haplotype reconstruction tools.

Conclusions:

HAT offers an effective solution for haplotype assembly.
The tool enhances the ability to reconstruct complex haplotypes, particularly in polyploid organisms.
HAT is available as an open-source tool for the research community.