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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: Mar 10, 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

Published on: August 20, 2021

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.

Peter Edge¹, Vineet Bafna¹, Vikas Bansal²

¹Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California 92053, USA.

Genome Research

|December 13, 2016

Summary

HapCUT2 is a new algorithm for haplotype assembly that accurately reconstructs individual genomes from diverse sequencing data. It efficiently handles multiple technologies, improving accuracy and scalability for whole-genome haplotype resolution.

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Last Updated: Mar 10, 2026

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Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

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Published on: June 28, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Haplotype assembly is crucial for understanding genetic variation and disease.
Existing computational tools struggle to scale across diverse sequencing technologies.
There is a growing need for robust methods to reconstruct whole-genome haplotypes.

Purpose of the Study:

To develop a novel algorithm, HapCUT2, for accurate and scalable haplotype assembly.
To extend existing methods to accommodate multiple sequencing technologies.
To improve whole-genome haplotype resolution from various data types.

Main Methods:

HapCUT2 algorithm development and implementation.
Simulations using diverse sequencing data types.
Application to whole-genome sequencing (WGS) data including dilution pool, linked-read, SMRT, and Hi-C sequencing.
Comparative analysis with existing haplotype assembly tools.

Main Results:

HapCUT2 demonstrates best-in-class accuracy across multiple sequencing technologies.
The algorithm scales effectively for high sequencing coverage and long-read WGS data.
HapCUT2 significantly improves error rates for Hi-C data by modeling specific error modalities.
High-resolution haplotypes with high pairwise phasing accuracy were achieved from Hi-C data.

Conclusions:

HapCUT2 is a robust and versatile tool for haplotype assembly.
The algorithm is applicable to a wide range of diverse sequencing technologies.
HapCUT2 advances the field of haplotype-resolved genome sequencing.