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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.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: May 20, 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

A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector.

Yan Guo¹, Yuwei Song², Limin Jiang³

¹Department of Public Health and Sciences, University of Miami, Miami, FL, USA. yxg835@med.miami.edu.

Nature Protocols

|March 27, 2025

Summary

This summary is machine-generated.

Inspector is a new tool for evaluating long-read DNA genome assemblies. It identifies and corrects errors, improving genome assembly quality and precision.

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Area of Science:

Genomics
Bioinformatics

Background:

Long-read sequencing generates extensive DNA sequences, crucial for assembling complex and repetitive genomic regions.
Despite advancements, genome assembly errors persist due to genomic complexity and technological limitations, necessitating robust evaluation methods.

Purpose of the Study:

To introduce Inspector, a versatile tool for evaluating long-read genome assemblies.
To highlight Inspector's capabilities in reference-free and reference-guided evaluation, error detection, and correction.

Main Methods:

Demonstration of four distinct procedures using Inspector for long-read assembly evaluation.
Utilizing Inspector's features for detecting small and large structural errors and performing haplotype-resolved analysis.

Main Results:

Inspector offers comprehensive assembly evaluation beyond basic statistics.
The tool precisely locates and categorizes various structural errors within genome assemblies.
Inspector's error correction feature enhances the quality of existing assemblies.

Conclusions:

Inspector provides a robust framework for evaluating long-read genome assemblies.
Its advanced features, including error correction and haplotype resolution, significantly improve assembly quality assessment.