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Related Concept Videos

Genome Annotation and Assembly03:36

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 Sequencing03:00

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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Sanger Sequencing01:57

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...
RNA-seq03:21

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 microarray-based...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Related Experiment Video

Updated: Jun 6, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

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

Limitations of next-generation genome sequence assembly.

Can Alkan1, Saba Sajjadian, Evan E Eichler

  • 1Department of Genome Sciences, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, Washington, USA.

Nature Methods
|November 25, 2010
PubMed
Summary
This summary is machine-generated.

High-throughput sequencing misses significant genomic data, including repeats and exons, in de novo genome assemblies. Combining high-throughput sequencing with high-quality approaches is crucial for accurate comparative genomics.

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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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Related Experiment Videos

Last Updated: Jun 6, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

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

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Area of Science:

  • Genomics
  • Comparative Biology
  • Bioinformatics

Background:

  • High-throughput sequencing (HTS) offers rapid genome delivery, transforming genetics and comparative biology.
  • De novo genome assembly is feasible but the limitations of short sequence reads are under-examined.

Purpose of the Study:

  • To evaluate the completeness of de novo genome assemblies generated using short reads.
  • To compare recent de novo assemblies against experimentally validated genomic features.

Main Methods:

  • Utilized the Short Oligonucleotide Analysis Package (SOAP) for de novo assembly.
  • Compared SOAP-generated assemblies from Han Chinese and Yoruban individuals to reference genomes and validated features.

Main Results:

  • De novo assemblies were 16.2% shorter than reference genomes.
  • Significant portions of common repeats (420.2 Mb) and duplicated sequences (99.1%) were missing.
  • Over 2,377 coding exons were completely absent from the assemblies.

Conclusions:

  • Sole reliance on short reads for de novo assembly leads to substantial data loss.
  • High-quality sequencing methods are essential alongside HTS for robust comparative genomics and evolutionary studies.