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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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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...

Next-generation Sequencing

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Although all next-generation methods use different technologies, they all share a set of standard features....

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Related Experiment Video

Updated: Jun 7, 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

GTasm: a genome assembly method using graph transformers and HiFi reads.

Junwei Luo¹, Ziheng Zhang¹, Xinliang Ma¹

¹School of Software, Henan Polytechnic University, Jiaozuo, China.

Frontiers in Genetics

|November 11, 2024

Summary

GTasm, a novel genome assembly method, utilizes graph transformer networks to improve genome sequence reconstruction. This approach enhances contiguity and accuracy, overcoming challenges posed by complex genomic repeats.

Keywords:

HiFi read deep learning genome assembly graph transformer sequencing technique

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Last Updated: Jun 7, 2025

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

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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Published on: May 6, 2010

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:

Accurate and complete chromosome-scale genome sequences are crucial for genomics.
Genome assembly is often fragmented due to complex repeat regions.
High-accuracy long reads improve genome assembly integrity.

Purpose of the Study:

To introduce GTasm, a new genome assembly method.
To leverage graph transformer networks for optimizing genome assembly.
To enhance the contiguity and accuracy of genome sequences.

Main Methods:

GTasm employs a graph transformer network on assembly graphs.
Features of vertices and edges are extracted.
A graph transformer model scores edges, and a heuristic algorithm finds optimal paths (contigs).
The model is trained using simulated HiFi reads (CHM13).

Main Results:

GTasm produces well-assembled genome sequences.
The method demonstrates strong performance on NA50 and NGA50 metrics.
Deep learning application improves assembly continuity and accuracy compared to other methods.

Conclusions:

GTasm offers an effective deep learning-based approach for genome assembly.
The method successfully addresses fragmentation challenges in genome reconstruction.
GTasm advances the field of computational genomics by improving assembly quality.