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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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Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences.

Gaik Tamazian¹, Pavel Dobrynin², Ksenia Krasheninnikova²

¹Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia. mail@gtamazian.com.

|August 24, 2016

Summary

Chromosomer rapidly arranges genome contigs into chromosomes using reference-based alignment. This tool aids genomic analysis for species lacking chromosome maps, offering valuable insights without mate-pair libraries.

Keywords:

Alignment Chromosome assembly Reference-assisted assembly

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Area of Science:

Genomics
Bioinformatics

Background:

Genome sequencing is rapidly expanding, increasing the need for accurate chromosome assembly.
De novo assembly methods are prone to errors from repetitive DNA sequences.
Reference-assisted assembly, using comparative inference, is a common approach for prokaryotic and eukaryotic genomes.

Purpose of the Study:

To develop a rapid, reference-based genome arrangement tool.
To facilitate chromosome assembly from contigs or scaffolds.
To provide auxiliary tools for genome assembly processes.

Main Methods:

Developed Chromosomer, a reference-based genome arrangement tool.
Utilizes alignments of genome contigs/scaffolds to a closely related reference genome.
Does not require mate-pair libraries.

Main Results:

Chromosomer rapidly builds chromosomes from genome contigs or scaffolds.
The tool offers auxiliary functions for common genome assembly operations.
Provides a straightforward alignment-based approach for chromosome arrangement.

Conclusions:

Chromosomer is a valuable tool for genomic analysis in species lacking chromosome maps.
Enables comparative genomic analysis, genomic variation assessment, and linkage group inference.
Facilitates mapping of contigs/scaffolds to high-quality reference assemblies.