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Genome Annotation and Assembly

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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: Nov 16, 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

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads.

Shien Huang¹, Xinyu He¹, Guohua Wang²

¹Group of Interdisciplinary Information Sciences, School of Software Engineering, Beijing Jiaotong University, China.

Briefings in Bioinformatics

|February 23, 2021

Summary

AlignGraph2 improves genome assembly from long sequencing reads using a similar genome-assisted reassembly method. This pipeline enhances contig accuracy and completeness for both error-prone and HiFi reads.

Keywords:

de Brujin graph genome assembly similar genome

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Last Updated: Nov 16, 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

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Area of Science:

Genomics
Bioinformatics

Background:

Third-generation sequencing long reads offer more complete genome assemblies than short reads.
Current long-read assembly algorithms struggle to achieve ideal accuracy and completeness.

Purpose of the Study:

To introduce AlignGraph2, a novel pipeline for similar genome-assisted reassembly of PacBio long reads.
To improve the accuracy and completeness of genome assemblies derived from long sequencing reads.

Main Methods:

AlignGraph2 utilizes a similar genome to guide the reassembly of long reads and preassembled contigs.
The pipeline incorporates four new algorithms: similarity-aware alignment, alignment filtration, reassembly, and weight-adjusted consensus.

Main Results:

AlignGraph2 significantly increases the alignment of long reads and bases compared to existing algorithms.
The pipeline effectively extends preassembled contigs, leading to improved N50 values and reduced indel rates.
AlignGraph2 demonstrates stable performance even with decreased genome similarity.

Conclusions:

AlignGraph2 offers a robust solution for enhancing long-read genome assembly through similar genome-assisted reassembly.
The software provides significant improvements in contig quality and assembly efficiency for both error-prone and HiFi long reads.