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Related Experiment Video

Updated: Oct 5, 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

DENTIST-using long reads for closing assembly gaps at high accuracy.

Arne Ludwig^1,2, Martin Pippel^1,2, Gene Myers^1,2

¹Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.

|January 25, 2022

Summary

DENTIST is a new automated method that accurately closes gaps in genome assemblies using long sequencing reads. This tool improves genome completeness and contiguity, outperforming previous methods in accuracy.

Keywords:

assembly gaps genome assembly long sequencing reads

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Last Updated: Oct 5, 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:

Short-read sequencing technologies often result in fragmented genome assemblies with gaps.
Existing gap-closing methods using long reads can introduce inaccuracies.
Improving genome assembly contiguity and completeness is crucial for genomic research.

Purpose of the Study:

To develop a highly accurate and automated pipeline for closing gaps in genome assemblies using long reads.
To enhance the contiguity and completeness of fragmented genome assemblies.
To provide a reliable method for accurate gap-filling in genomic data.

Main Methods:

Developed DENTIST, an automated pipeline for gap closure in short-read assemblies with long, error-prone reads.
Implemented comprehensive determination of repetitive regions for unambiguous long-read alignment.
Integrated a consensus sequence computation for high base accuracy and validated closed gaps.
Utilized realistic benchmark datasets for Drosophila, Arabidopsis, hummingbird, and human genomes.

Main Results:

DENTIST demonstrated substantially higher accuracy in closing assembly gaps compared to previous methods.
The method achieved high sensitivity in gap closure across various genome sizes.
Validated accuracy of closed gaps using simulated and real PacBio continuous long reads.
DENTIST consistently improved genome assembly contiguity and completeness.

Conclusions:

DENTIST offers an accurate and automated solution for improving genome assembly contiguity and completeness using long reads.
The pipeline provides a significant advancement over existing gap-closing techniques.
Source code and benchmark datasets are publicly available for reproducibility and future research.