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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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
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RNA-seq03:21

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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. 
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Maxam-Gilbert Sequencing01:05

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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

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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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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Related Experiment Video

Updated: Apr 5, 2026

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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SpeedSeq: ultra-fast personal genome analysis and interpretation.

Colby Chiang1,2, Ryan M Layer3,4, Gregory G Faust2

  • 1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.

Nature Methods
|August 11, 2015
PubMed
Summary

SpeedSeq is an open-source genome analysis platform that significantly reduces human genome analysis time to 13 hours. This bioinformatics tool provides efficient variant detection and interpretation, overcoming previous computational bottlenecks.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Bioinformatics pipelines for genome analysis are computationally intensive.
  • Current methods often require weeks of computation and expert involvement.
  • There is a need for faster and more accessible genome analysis tools.

Purpose of the Study:

  • To introduce SpeedSeq, an open-source genome analysis platform.
  • To demonstrate SpeedSeq's efficiency in analyzing a 50× human genome.
  • To highlight SpeedSeq's capabilities in variant detection and interpretation.

Main Methods:

  • Development of an open-source genome analysis platform named SpeedSeq.
  • Utilized a low-cost server for genome-wide analysis.
  • Implemented algorithms for alignment, variant detection, and functional annotation.

Main Results:

  • SpeedSeq analyzed a 50× human genome in 13 hours.
  • Achieved performance competitive with or superior to existing methods.
  • Successfully detected germline and somatic single-nucleotide variants, structural variants, insertions, and deletions.
  • Included novel functionality for streamlined interpretation.

Conclusions:

  • SpeedSeq alleviates the bioinformatics bottleneck associated with large-scale genome analysis.
  • The platform offers a cost-effective and efficient solution for genome analysis.
  • SpeedSeq enables faster and more streamlined interpretation of genomic variants.