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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...

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Related Experiment Video

Updated: Nov 6, 2025

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

NGScloud2: optimized bioinformatic analysis using Amazon Web Services.

Fernando Mora-Márquez¹, José Luis Vázquez-Poletti², Unai López de Heredia¹

¹GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain.

|May 7, 2021

Summary

This summary is machine-generated.

NGScloud2 is an updated bioinformatic system for cloud-based RNA sequencing analysis, offering cost savings and expanded tools for various genomic applications. It provides accessible infrastructure for complex data analysis.

Keywords:

AWS Bioinformatics Cloud computing Functional annotation Next generation sequencing Transcriptomics

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Last Updated: Nov 6, 2025

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

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

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

Published on: April 8, 2017

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

NGScloud was an early cloud-based system for de novo RNAseq analysis of non-model species.
Rapid advancements in cloud computing and bioinformatics tools rendered NGScloud obsolete.
NGScloud2 has been developed to address these limitations and provide an updated solution.

Purpose of the Study:

To present NGScloud2, an enhanced bioinformatic system for cloud-based genomic data analysis.
To enable efficient and cost-effective analysis of various next-generation sequencing data types.
To provide accessible cloud computing infrastructure for researchers lacking specialized hardware.

Main Methods:

NGScloud2 leverages cloud computing infrastructure, specifically Amazon Web Services (AWS), with optimized instance types and spot instance capabilities for cost savings.
The system incorporates updated and common applications for de novo RNAseq analysis.
It includes tools for reference-based RNAseq, RADseq, and functional annotation workflows.

Main Results:

NGScloud2 successfully processed pipelines for de novo RNAseq, reference-based RNAseq, RADseq, and functional annotation using real experimental data.
Workflow performance estimates and optimization tips are provided.
A qualitative comparison with the Galaxy framework is presented.

Conclusions:

NGScloud2 offers an enhanced and expanded platform for cloud-based genomic data analysis, improving upon its predecessor.
The system optimizes access to large-scale computing resources, making advanced bioinformatic tools accessible to a wider range of users.
Code and companion utilities are publicly available to facilitate adoption and downstream analysis.