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Related Concept Videos

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...
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.
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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.
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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...

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Related Experiment Video

Updated: Jun 10, 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

Unlocking short read sequencing for metagenomics.

Sébastien Rodrigue1, Arne C Materna, Sonia C Timberlake

  • 1Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachussetts, United States of America.

Plos One
|August 3, 2010
PubMed
Summary

This study introduces a novel sequencing method combining short-read technology with a computational pipeline to generate long, high-quality reads cost-effectively. This advance benefits applications requiring both high throughput and extended read lengths, such as metagenomic analysis.

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Last Updated: Jun 10, 2026

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: February 24, 2015

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • High-throughput sequencing platforms face a trade-off between read count/cost and read length.
  • Existing methods limit the ability to achieve both high throughput and long reads simultaneously.

Purpose of the Study:

  • To develop a cost-effective method for generating long, high-quality sequencing reads.
  • To overcome the limitations of current short-read sequencing technologies.

Main Methods:

  • An automatable, gel-less library construction protocol was developed.
  • Paired-end sequencing was performed on a short-read instrument.
  • The SHERA software package was created to join overlapping mate-pair sequences into longer composite reads.

Main Results:

  • Millions of reads exceeding 200 bp were generated with quality scores comparable to Sanger sequencing.
  • The method successfully produced overlapping mate-pair sequences for composite read generation.
  • The pipeline demonstrated low error rates in metagenomic analyses.

Conclusions:

  • The developed strategy is broadly applicable to sequencing applications needing longer reads at high throughput.
  • This approach enables cost-effective metagenomic analyses using the Illumina Genome Analyzer.
  • The method offers a significant cost reduction compared to traditional pyrosequencing.