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Related Experiment Video

Updated: Apr 28, 2026

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

Ragout-a reference-assisted assembly tool for bacterial genomes.

Mikhail Kolmogorov¹, Brian Raney², Benedict Paten²

¹St. Petersburg University of the Russian Academy of Sciences, Bioinformatics Institute, St. Petersburg, Russia, UCSC, 1156 High Street, Santa Cruz, CA and Department of Computer Science and Engineering, UCSD, 9500 Gilman Drive, La Jolla, CA, USASt. Petersburg University of the Russian Academy of Sciences, Bioinformatics Institute, St. Petersburg, Russia, UCSC, 1156 High Street, Santa Cruz, CA and Department of Computer Science and Engineering, UCSD, 9500 Gilman Drive, La Jolla, CA, USA.

Bioinformatics (Oxford, England)

|June 17, 2014

Summary

Ragout improves bacterial genome assembly by using multiple related genomes to order contigs. This approach, using short-read sequencing data, can generate a single, high-quality chromosome scaffold for common bacterial species.

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Last Updated: Apr 28, 2026

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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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

High-throughput short-read sequencing often yields fragmented bacterial genome assemblies with numerous contigs.
Existing methods to improve assemblies, like long reads or jumping libraries, are costly and have high error rates.
Complete genomes from closely related species/strains offer a potential avenue for enhancing assembly quality.

Purpose of the Study:

To develop a novel genome rearrangement approach for improving bacterial genome assemblies.
To leverage multiple related reference genomes and their evolutionary relationships to correctly order contigs.
To reduce assembly gaps and improve scaffold contiguity using assembly graphs and synteny blocks.

Main Methods:

Developed Ragout, a genome rearrangement algorithm.
Utilized multiple reference genomes and their evolutionary relationships to guide contig ordering.
Incorporated assembly graphs and multi-scale synteny blocks to bridge gaps caused by small contigs.

Main Results:

Ragout effectively improves bacterial genome assembly quality.
The method successfully orders contigs using multiple references and evolutionary information.
Ragout reduces assembly gaps, leading to more contiguous scaffolds.
Demonstrated effectiveness in both simulations and real datasets for common bacterial species.

Conclusions:

Ragout offers a cost-effective solution for high-quality bacterial genome assembly.
For common bacterial species with available related genomes, short-read sequencing combined with Ragout can yield a single chromosome scaffold.
This approach enhances the utility of existing short-read sequencing data for bacterial genomics.