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.

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

A comprehensive reference genome assembly dataset of birds inhabiting Denmark, Greenland, and the Faroe Islands.

GigaScience·2026

Same author

The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.

Animal microbiome·2026

Same author

Song complexity in suboscine birds: evolutionary drivers and ecological constraints.

Proceedings. Biological sciences·2026

Same author

Draft assemblies for 177 bird species enhance genus-level coverage.

GigaScience·2026

Same author

Vaginal Microbiome Is Associated with Breed and Pregnancy Status in Beef Cattle.

Animals : an open access journal from MDPI·2026

Same author

Spatial Patterns of Intraspecific Genetic Diversity Follow no General Rule Across Climatic and Geographic Gradients.

Molecular ecology·2026

Search research articles

Related Experiment Video

Updated: Jun 1, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

PRGmatic: an efficient pipeline for collating genome-enriched second-generation sequencing data using a

Sarah M Hird¹, Robb T Brumfield, Bryan C Carstens

¹Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA. shird1@tigers.lsu.edu

Molecular Ecology Resources

|June 17, 2011

Summary

This study presents an open-source pipeline simplifying population genetic analysis using second-generation sequencing data. It enables labs without bioinformaticians to analyze genomic data, providing essential population genetics and phylogeography insights.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 1, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

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

Area of Science:

Genomics
Population Genetics
Bioinformatics

Background:

Second-generation sequencing (SGS) combined with genome enrichment is vital for population genetic and phylogeographic studies.
Analyzing SGS data requires a complex and time-consuming assembly of multiple bioinformatics tools.
Research labs often lack dedicated bioinformaticians, hindering the use of SGS data.

Purpose of the Study:

To develop a user-friendly, open-source pipeline for analyzing second-generation sequencing data.
To enable research laboratories without specialized bioinformatics support to perform population genetic and phylogeographic analyses.
To streamline the process of preparing and analyzing large-scale genomic datasets.

Main Methods:

Assembled a suite of bioinformatics programs (CAP3, BWA, SAMtools, VarScan) into an automated pipeline.
Utilized Perl scripting to connect the programs, creating a cohesive workflow.
Developed a pipeline that does not require a reference genome, constructing its own.
Input: FASTA-formatted sequencing reads sorted by individual. Output: Multi-FASTA files per locus, summary statistics.

Main Results:

Successfully created a pipeline that processes second-generation sequencing reads into locus-specific multi-FASTA files.
Generated summary files including heterozygosity, allele calls, and population genetics statistics (e.g., Theta, Tajima's D).
The pipeline allows user-defined parameter adjustments for programs like minimum coverage, enhancing data quality control.

Conclusions:

The developed pipeline significantly lowers the barrier for utilizing second-generation sequencing data in population genetics and phylogeography.
Empowers research groups lacking dedicated bioinformaticians to conduct advanced genomic analyses.
Facilitates robust evaluation of data quality and nature prior to downstream analyses.