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

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.

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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....

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...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

You might also read

Related Articles

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

Sort by

Same author

The role of gut microbiome in the pathophysiology of PTSD, depression, and anxiety disorders.

Gut microbes reports·2026

Same author

Being friendly to the skin microbiome: Experimental assessment.

Frontiers in microbiomes·2026

Same author

Preliminary Insights Into the Relationship Between the Gut Microbiome and Host Genome in Posttraumatic Stress Disorder.

Genes, brain, and behavior·2025

Same author

Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity.

Gut microbiome (Cambridge, England)·2024

Same author

The butyrate-producing and spore-forming bacterial genus <i>Coprococcus</i> as a potential biomarker for neurological disorders.

Gut microbiome (Cambridge, England)·2024

Same author

GUT MICROBIOME DIVERSITY OF THREE RHINOCEROS SPECIES IN EUROPEAN ZOOS.

Journal of zoo and wildlife medicine : official publication of the American Association of Zoo Veterinarians·2024

Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026

Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 27, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.

Marten Boetzer, Walter Pirovano¹

¹BaseClear B,V,, Genome analysis and technology department, Einsteinweg 5, Leiden 2333 CC, The Netherlands. walter.pirovano@baseclear.com.

BMC Bioinformatics

|June 22, 2014

Summary

This summary is machine-generated.

Pacific Biosciences long reads significantly improve genome assembly by scaffolding contigs. Our SSPACE-LongRead software efficiently creates nearly complete bacterial genomes using this technology.

More Related Videos

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Related Experiment Videos

Last Updated: Apr 27, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Next Generation Sequencing (NGS) often yields incomplete draft genomes.
Pacific Biosciences (PacBio) RS single molecule sequencing offers long reads to improve assembly quality.
Scaffolding is crucial for enhancing the accuracy and completeness of draft genome assemblies.

Purpose of the Study:

To develop a hybrid assembly method for scaffolding pre-assembled contigs using PacBio RS long reads.
To assess the effectiveness of the proposed methodology in reducing contig count and improving genome completeness.
To introduce the SSPACE-LongRead software for upgrading draft genomes.

Main Methods:

A novel hybrid assembly methodology was developed.
PacBio RS long read information was used as a backbone to scaffold pre-assembled contigs iteratively.
The method was tested on six bacterial draft genomes assembled with Illumina MiSeq or Roche 454 data.

Main Results:

Even 50× coverage of uncorrected PacBio RS long reads drastically reduced the number of contigs.
The proposed strategy demonstrated superior performance compared to the AHA scaffolder.
Nearly complete bacterial genomes were produced using the new methodology.

Conclusions:

SSPACE-LongRead software upgrades incomplete draft genomes using single molecule sequences.
PacBio sequencing technology advances enable fast and reliable genome scaffolding.
The software requires limited computational resources, making genome scaffolding accessible.