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

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...

You might also read

Related Articles

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

Sort by

Same author

Detecting introgression from phylogenetic invariant site patterns using machine learning.

Applications in plant sciences·2026

Same author

A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants.

Annals of botany·2026

Same author

Geography and admixture shape the genome-scale phylogeny of North American Delphinium.

The New phytologist·2026

Same author

Estimating Waiting Distances between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent.

Systematic biology·2025

Same author

Small snakes, big cities: Population genetics of urban Dekay's brown snake (Storeria dekayi) in New Jersey.

The Journal of heredity·2025

Same author

Pleistocene island connectivity did not enhance dispersal or impact population size change in Galápagos geckos.

Proceedings. Biological sciences·2025

Search research articles

Related Experiment Video

Updated: Dec 31, 2025

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Published on: November 30, 2014

ipyrad: Interactive assembly and analysis of RADseq datasets.

Deren A R Eaton¹, Isaac Overcast²

¹Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA.

Bioinformatics (Oxford, England)

|January 7, 2020

Summary

ipyrad is a free and open-source tool for analyzing restriction site-associated DNA sequencing data. This scalable software can be used for de novo or reference-based assembly and downstream analyses.

More Related Videos

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

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

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

Published on: August 18, 2023

Related Experiment Videos

Last Updated: Dec 31, 2025

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Published on: November 30, 2014

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

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

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

Published on: August 18, 2023

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Restriction site-associated DNA (RAD) sequencing is a powerful method for population genomics.
Analyzing RAD sequencing data requires specialized bioinformatics tools for assembly and variant calling.

Purpose of the Study:

To introduce ipyrad, a new open-source software for assembling and analyzing RAD sequencing data.
To provide a scalable and flexible tool for researchers working with large RAD datasets.

Main Methods:

ipyrad utilizes both de novo and reference-based approaches for RAD data assembly.
The software is designed for massive scalability, supporting hundreds of taxa and thousands of samples.
ipyrad can be efficiently parallelized on high-performance computing clusters.

Main Results:

ipyrad offers a command-line interface and a Python package for versatile use.
The Python API allows for interactive scripting and integration with downstream analysis tools.
The tool is freely available with comprehensive documentation and tutorials.

Conclusions:

ipyrad provides a robust, scalable, and user-friendly solution for RAD sequencing data analysis.
Its flexibility and accessibility make it a valuable resource for population genomics research.