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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.

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Updated: May 12, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.

Sebastiaan van Heesch¹, Wigard P Kloosterman, Nico Lansu

¹Hubrecht Institute/KNAW and University Medical Center Utrecht, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands.

|April 18, 2013

Summary

This summary is machine-generated.

Mate-pair sequencing libraries with optimized insert sizes significantly improve genome assembly scaffolding by spanning repetitive elements. This approach enhances genome coverage and aids in finishing draft mammalian genomes.

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Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Area of Science:

Genomics
Bioinformatics

Background:

Paired-tag sequencing is vital for genome structure analysis.
Mammalian genomes present challenges due to complex organization and repetitive elements.

Purpose of the Study:

To assess the utility of various next-generation sequencing libraries for genome coverage and scaffolding.
To improve the analysis of mammalian genome structure and repetitive elements.

Main Methods:

Systematic assessment of paired-end and mate-pair (MP) libraries with insert sizes from 170 bp to 25 kb.
Evaluation of library utility for genome coverage and scaffolding in Rattus norvegicus.
Analysis of medium- and large-insert MP libraries for genome structure analysis.

Main Results:

Large-insert MP libraries (20-25 kb) offered high physical genome coverage and spanned repetitive elements effectively.
Medium-sized MP libraries (5-15 kb) were more efficient for genome structure analysis than shorter libraries.
Combining medium- and large-insert libraries increased scaffolding N50 by 3-fold.
Data improved contig order and orientation in the rat reference genome assembly.

Conclusions:

Mate-pair libraries with insert sizes tailored to repetitive element distributions enhance contig scaffolding.
This strategy contributes to the finishing of draft mammalian genomes.