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

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Related Experiment Video

Updated: Jun 10, 2025

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.

Mir Henglin^1,2, Maryam Ghareghani^3,4, William T Harvey⁵

¹Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.

|October 10, 2024

Summary

This summary is machine-generated.

Graphasing is a new workflow for creating de novo haplotype-resolved genome assemblies. It combines Strand-seq and assembly graphs, offering high accuracy for genetic research without parental data.

Keywords:

Assembly graph De novo assembly Haplotype Hi-C Hifiasm Phasing Strand-seq Trio Verkko

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Area of Science:

Genomics and Bioinformatics
Population Genetics
Molecular Biology

Background:

Haplotype information is essential for understanding genetic variation in biomedical and population genetics.
Existing methods for de novo haplotype-resolved assemblies often rely on parental data or intermediate collapsed assemblies, posing significant challenges.

Purpose of the Study:

To introduce Graphasing, a novel computational workflow for generating chromosome-scale de novo haplotype-resolved assemblies for diploid genomes.
To demonstrate the integration capabilities of Graphasing with existing assembly pipelines that produce assembly graphs and support haplotype assembly.

Main Methods:

Graphasing synthesizes the global phase information from Strand-seq data with the topology of assembly graphs.
The workflow is designed to be compatible with any assembly pipeline that outputs an assembly graph and includes a haplotype assembly mode.

Main Results:

Graphasing achieves contiguity, phasing accuracy, and assembly quality comparable to trio phasing methods.
The workflow demonstrates superior phasing accuracy compared to Hi-C based methods.
Graphasing successfully generated human assemblies with more than 18 chromosome-spanning haplotypes.

Conclusions:

Graphasing provides an effective and accurate approach for de novo haplotype resolution in diploid genomes.
This method overcomes limitations of previous strategies by not requiring parental data and offering high phasing accuracy.
Graphasing represents a significant advancement for genomic research, enabling more comprehensive haplotype analysis.