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Updated: Dec 12, 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

HASLR: Fast Hybrid Assembly of Long Reads.

Ehsan Haghshenas¹, Hossein Asghari¹, Jens Stoye²

¹School of Computing Science, Simon Fraser University, Burnaby, BC V5A1S6, Canada; Vancouver Prostate Centre, Vancouver, BC V6H3Z6, Canada.

|August 12, 2020

Summary

HASLR is a new hybrid genome assembler. It efficiently creates accurate genome assemblies using long and short sequencing reads, outperforming other methods in speed and accuracy.

Keywords:

Bioinformatics Genomics Sequence Analysis

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Last Updated: Dec 12, 2025

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

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Published on: August 20, 2021

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Third-generation sequencing (TGS) technologies, like Oxford Nanopore and Pacific Biosciences, enable more contiguous genome assemblies.
TGS long reads help overcome challenges posed by repetitive DNA sequences.
Current accurate long-read assemblers are computationally intensive, while faster methods lack precision.

Purpose of the Study:

To develop an efficient and accurate hybrid genome assembler.
To leverage both error-prone long reads and high-quality short reads for improved assembly.

Main Methods:

Developed HASLR, a novel hybrid assembler.
Utilized a combination of long reads (e.g., from TGS) and short reads for genome assembly.
Evaluated HASLR's performance against existing assemblers.

Main Results:

HASLR demonstrated superior speed compared to other assemblers.
HASLR achieved the lowest number of misassemblies across most tested samples.
The assembler maintained contiguity and accuracy comparable to existing methods.

Conclusions:

HASLR offers an efficient and accurate solution for genome assembly.
The hybrid approach effectively utilizes the strengths of both long and short sequencing reads.
This method addresses the computational cost and accuracy trade-offs in current assembly tools.