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

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...
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...
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.
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

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 primer.
Since the...

You might also read

Related Articles

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

Sort by
Same author

Intrinsic differences in hamster and mouse macrophage biology correlate with susceptibility to Leishmania donovani infection.

Journal of leukocyte biology·2026
Same author

Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus <i>Leishmania</i> hybrid.

NAR molecular medicine·2026
Same author

Segmented filamentous bacteria are worldwide human gut commensals.

Nature communications·2026
Same author

Genome Sequencing of Leishmania tropica in Tissues of Moroccan Patients Reveals Microfocal Transmission Underlain by (Pseudo)Clonal and Sexual Reproduction.

The Journal of infectious diseases·2025
Same author

Correction: Gene deletion as a possible strategy adopted by New World Leishmania infantum to maximize geographic dispersion.

PLoS pathogens·2025
Same author

Cross-subgenus hybridization between <i>Leishmania</i> and <i>Sauroleishmania</i> informs on parasite genomic compatibility and transcriptomic adaptation.

bioRxiv : the preprint server for biology·2025
Same journal

Distinct repeat architecture landscapes in the proteomes of protozoan parasites.

NAR genomics and bioinformatics·2026
Same journal

Long non-coding RNA triplex-dependent regulation of melanoma gene networks.

NAR genomics and bioinformatics·2026
Same journal

Challenges in predicting chromatin accessibility differences between species.

NAR genomics and bioinformatics·2026
Same journal

Power-law penalties correct distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions.

NAR genomics and bioinformatics·2026
Same journal

Correction to 'Genome sequence assembly and annotation of <i>MATA</i> and <i>MATB</i> strains of <i>Yarrowia lipolytica'</i>.

NAR genomics and bioinformatics·2026
Same journal

Comprehensive mapping of identical sequences across human proteins emphasizes the widespread issue of shared epitopes in self-antigens.

NAR genomics and bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jun 26, 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

LORA: a polymorphic multi-sample long read assembly pipeline.

Dimitri Desvillechabrol1,2, Rania Ouazahrou1,2, Juliana Pipoli da Fonseca3

  • 1Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France.

NAR Genomics and Bioinformatics
|June 25, 2026
PubMed
Summary
This summary is machine-generated.

LORA is a new, user-friendly application for genome assembly using long-read sequencing data. It integrates multiple tools and quality checks, ensuring reproducible and high-quality genomic results for diverse species.

More Related Videos

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
11:04

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Related Experiment Videos

Last Updated: Jun 26, 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

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
11:04

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Long-read sequencing is crucial for high-contiguity genome assembly, especially for complex genomic regions.
  • Existing genome assemblers vary in performance and reproducibility, posing challenges for researchers.
  • The need for standardized, reproducible workflows in genome assembly is critical.

Purpose of the Study:

  • To develop LORA, an easy-to-use and reproducible application for genome assembly from long-read sequencing data.
  • To integrate multiple established and novel genome assembly tools into a single pipeline.
  • To provide comprehensive quality assessment and reporting features for genome assemblies.

Main Methods:

  • LORA is implemented as a Snakemake pipeline for parallel task execution and cluster compatibility.
  • It integrates assemblers such as Canu, HiFiasm, Flye, Unicycler, Necat, and Pecat.
  • Includes quality assessment, interactive HTML reports, taxonomic identification (BLAST), and completeness evaluation.

Main Results:

  • Demonstrated LORA's capability in assembling bacterial and unicellular eukaryotic genomes using PacBio and Oxford Nanopore data.
  • Highlighted typical outcomes and common pitfalls in long-read genome assembly workflows.
  • Provided a comprehensive view of assembly quality and potential issues through integrated reporting.

Conclusions:

  • LORA offers a reproducible and comprehensive solution for long-read genome assembly.
  • The application facilitates the interpretation of assembly quality and identification of potential problems.
  • LORA is part of the Sequana project, promoting reproducibility and ease of deployment.