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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Related Experiment Video

Updated: Apr 26, 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

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Enly: Improving Draft Genomes through Reads Recycling.

Marco Fondi¹, Valerio Orlandini¹, Giorgio Corti²

¹1. Dept. of Evolutionary Biology, Via Madonna del Piano 6, 50143 Sesto Fiorentino,Florence, Italy;

Journal of Genomics

|July 18, 2014

Summary

Enly is a new tool that closes genome gaps by mapping sequence reads to contig edges. This method successfully reduced gaps in draft genomes by up to 20%, improving genomic analysis.

Keywords:

454.Contig extension Genome assembly Newbler Next Generation Sequencing

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Completing genome sequences is crucial for comparative, functional, and evolutionary genomics.
Current methods for genome completion can be time-consuming and resource-intensive.
High-throughput sequencing and de novo assembly generate draft genomes with gaps.

Purpose of the Study:

To develop an efficient tool for extending genomic contigs and closing gaps in draft genomes.
To improve the quality of de novo genome assemblies.

Main Methods:

Enly utilizes iterative mapping of sequence reads to contig edges.
The tool is designed to extend genomic contigs, particularly those from Newbler-like assemblies.
Enly is a cross-platform tool with parallelizable pipeline steps.

Main Results:

Testing Enly on de novo draft genomes resulted in the closure of up to 20% of existing gaps.
The tool effectively extends genomic contigs derived from high-throughput sequencing data.
Enly demonstrated significant improvements in draft genome quality.

Conclusions:

Enly provides a simple and effective solution for genome gap closure.
The tool accelerates the process of improving draft genomes from de novo assemblies.
Enly enhances the utility of genomic data for various downstream analyses.