Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.4K
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.
19.4K
Sanger Sequencing01:57

Sanger Sequencing

759.6K
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...
759.6K
RNA-seq03:21

RNA-seq

10.5K
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...
10.5K
Next-generation Sequencing03:00

Next-generation Sequencing

93.2K
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....
93.2K
Genomics02:02

Genomics

37.8K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
37.8K
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

6.6K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
6.6K

You might also read

Related Articles

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

Sort by
Same author

High-Resolution Genomic Surveillance of Carbapenem-Resistant <i>Acinetobacter baumannii</i>: IC-2 Clonal Diversity, Resistance Determinants, and Virulence Signatures.

Antibiotics (Basel, Switzerland)·2026
Same author

Severe Mycoplasma pneumoniae Pneumonia During the 2023-2024 European Re-Emergence: Why Severity Does Not Predict Macrolide Resistance.

Antibiotics (Basel, Switzerland)·2026
Same author

Divergent Avian Influenza H10 Viruses from Sympatric Waterbird Species in Italy: Zoonotic Potential Assessment by Molecular Markers.

Microorganisms·2025
Same author

Resurgence of <i>Bordetella pertussis</i> in Lazio: A Cross-Age Surveillance Study from Two Referral Hospitals.

Microorganisms·2025
Same author

Molecular investigation on measles cases rise and variants co-circulation in the Lazio region, Italy.

Virology journal·2025
Same author

One-Year Monitoring of the Evolution of SARS-CoV-2 Omicron Subvariants Through Wastewater Analysis (Central Italy, August 2023-July 2024).

Life (Basel, Switzerland)·2025

Related Experiment Video

Updated: Sep 29, 2025

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

17.6K

The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study.

Martina Rueca1, Emanuela Giombini1, Francesco Messina2

  • 1Laboratory of Virology and Biosafety Laboratories National Institute for Infectious Diseases "Lazzaro Spallanzani" Istituto di Ricovero e Cura a Carattere Scientifico Rome Italy.

JMIR Bioinformatics and Biotechnology
|March 21, 2022
PubMed
Summary
This summary is machine-generated.

The Easy-to-use SARS-CoV-2 Assembler (ESCA) pipeline provides rapid, high-quality genome assembly from next-generation sequencing data. This tool aids in identifying SARS-CoV-2 variants with minimal bioinformatics expertise.

Keywords:
COVID-19NGS data analysisSARS-CoV-2 genomealgorithmsbioinformaticbioinformatics tooldigital toolsgenomehealth informatics

More Related Videos

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.0K
Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.7K

Related Experiment Videos

Last Updated: Sep 29, 2025

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

17.6K
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.0K
Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.7K

Area of Science:

  • Genomics
  • Bioinformatics
  • Virology

Background:

  • Early sequencing of the SARS-CoV-2 genome was crucial for understanding COVID-19 dynamics and developing global countermeasures.
  • Amplicon-based next-generation sequencing (NGS) is vital for tracking SARS-CoV-2 variants, including those with deletions and mutations.

Purpose of the Study:

  • To introduce the Easy-to-use SARS-CoV-2 Assembler (ESCA) pipeline for streamlined analysis of amplicon-based NGS data.
  • To provide a user-friendly tool for SARS-CoV-2 genome assembly and variant identification.

Main Methods:

  • Development of the Easy-to-use SARS-CoV-2 Assembler (ESCA) pipeline.
  • Application of ESCA to Ion Torrent and Illumina raw sequencing data.

Main Results:

  • ESCA achieved high-quality SARS-CoV-2 genome assembly from diverse NGS platforms.
  • The pipeline effectively assists users in correcting low-coverage regions.
  • ESCA facilitates comparison of multisample assembled genomes in a tabular format.

Conclusions:

  • ESCA automatically generates variant table outputs, enabling rapid identification of SARS-CoV-2 variants of interest.
  • The ESCA pipeline offers a complete, rapid, and accurate analysis solution, accessible even to users with limited bioinformatics knowledge.