Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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

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.

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...

RNA-seq

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs.

Microbial genomics·2019

Same author

Prospective genomic surveillance of methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013.

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin·2019

Same author

One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock.

mBio·2019

Same author

Separating Bacteria by Capsule Amount Using a Discontinuous Density Gradient.

Journal of visualized experiments : JoVE·2019

Same author

Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States.

PloS one·2019

Same author

Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.

The Journal of antimicrobial chemotherapy·2019

Search research articles

Related Experiment Video

Updated: May 25, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

BamView: visualizing and interpretation of next-generation sequencing read alignments.

Tim Carver¹, Simon R Harris, Thomas D Otto

¹Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. artemis@sanger.ac.uk

Briefings in Bioinformatics

|January 19, 2012

Summary

BamView is a desktop application for visualizing and analyzing next-generation sequencing (NGS) data. It aids in exploring aligned reads, identifying SNPs, and discovering structural variations within genomic data.

More Related Videos

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

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

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

Published on: April 4, 2018

Related Experiment Videos

Last Updated: May 25, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

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

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

Published on: April 4, 2018

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Next-generation sequencing (NGS) enables large-scale, low-cost DNA sequencing.
Analyzing NGS data requires specialized tools for visualization and interpretation.
Existing tools may lack comprehensive features for detailed NGS data exploration.

Purpose of the Study:

To develop BamView, a desktop application for visualizing and analyzing NGS sequence reads aligned to a reference genome.
To provide tools for in-depth investigation of NGS data, including base quality, coverage, and alignment comparisons.
To facilitate the discovery of genetic variations such as SNPs and structural rearrangements.

Main Methods:

BamView is a desktop application that visualizes aligned NGS reads.
It offers multiple levels of magnification, from nucleotide to genome level.
Features include overlaying multiple alignment files, applying filters, and integrating with the Artemis genome browser.

Main Results:

BamView allows detailed examination of aligned reads, including base qualities and overall coverage.
Users can compare results from different experiments by overlaying alignment files.
The software highlights single nucleotide polymorphism (SNP) density and candidate SNP sites.
Read-pair information aids in discovering large structural insertions and deletions.
Simple analyses like read counts and RPKM for selected genes are calculated.

Conclusions:

BamView provides a comprehensive platform for visualizing and analyzing next-generation sequencing data.
Its integration with Artemis allows for contextual study of NGS data within the reference genome.
The tool facilitates the identification of genetic variations and structural anomalies, aiding biological discovery.