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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 29, 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

Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.

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

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

Biorxiv : the Preprint Server for Biology

|March 26, 2024

Summary

This summary is machine-generated.

Graphasing generates de novo haplotype-resolved genome assemblies using Strand-seq and assembly graphs. This method achieves high accuracy and contiguity without parental data, outperforming existing techniques.

Keywords:

Assembly Graph Haplotype Hi-C Phasing Strand-seq Trio Verkko de-novo Assembly hifiasm

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Area of Science:

Genomics
Bioinformatics
Population Genetics

Background:

Haplotype information is vital for biomedical and population genetics.
Current de novo haplotype assembly methods often require parental data or intermediate collapsed assemblies.

Purpose of the Study:

To present Graphasing, a novel workflow for de novo haplotype-resolved genome assembly.
To enable chromosome-scale haplotype generation for diploid genomes without parental data.

Main Methods:

Graphasing synthesizes Strand-seq phase signals with assembly graph topology.
The workflow integrates with existing assembly pipelines that output assembly graphs and support haplotype assembly.

Main Results:

Graphasing achieves comparable contiguity, phasing accuracy, and assembly quality to trio-phasing.
It outperforms Hi-C in phasing accuracy.
Generates human assemblies with over 18 chromosome-spanning haplotypes.

Conclusions:

Graphasing provides an efficient and accurate method for de novo haplotype-resolved genome assembly.
It overcomes limitations of existing strategies, particularly the need for parental data.