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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.

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...

Sanger Sequencing

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...

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Related Experiment Video

Updated: May 11, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

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Published on: May 9, 2017

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation

Hideki Nagasaki¹, Takako Mochizuki, Yuichi Kodama

¹Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8510, Japan.

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes

|May 10, 2013

Summary

The DDBJ Read Annotation Pipeline offers a free, cloud-based solution for analyzing next-generation sequencing (NGS) data. This user-friendly tool simplifies complex genomic analysis for molecular biologists using NIG supercomputers.

Keywords:

analytical pipeline cloud computing genome analysis next-generation sequencing sequence read archive

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Published on: May 9, 2017

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Next-generation sequencing (NGS) generates vast amounts of data, posing computational challenges for molecular biologists.
Access to suitable hardware and computational expertise is often limited, hindering genomic research.

Purpose of the Study:

To introduce the DDBJ Read Annotation Pipeline (DDBJ Pipeline), a cloud-based system for high-throughput NGS data analysis.
To provide molecular biologists with a user-friendly platform for complex genomic annotations.

Main Methods:

Development of a cloud computing-based analytical pipeline utilizing NIG supercomputers.
Implementation of a graphical web interface for user accessibility.
Integration of two analysis components: basic (mapping, assembly) and high-level (functional annotation).

Main Results:

The DDBJ Pipeline enables high-throughput annotation of NGS reads through decentralized processing.
Users can seamlessly transition between basic and advanced analysis components.
Direct import of public NGS data from DDBJ Sequence Read Archive via accession number is supported.

Conclusions:

The DDBJ Pipeline facilitates NGS data analysis by providing unified workflows on a supercomputer.
This resource democratizes advanced genomic analysis for researchers without extensive computational resources.
The pipeline is freely accessible at http://p.ddbj.nig.ac.jp/.