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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.

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...

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.

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

Genomic DNA in Prokaryotes

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...

Prokaryotic Gene Structure and Organization

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...

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Related Experiment Video

Updated: Jun 10, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

Matt J Cahill¹, Claudio U Köser, Nicholas E Ross

¹Department of Genetics, University of Cambridge, Cambridge, United Kingdom.

|July 17, 2010

Summary

This summary is machine-generated.

Short next-generation sequencing reads can assemble many prokaryote genomes, but repeat regions pose challenges. A new method predicts assembly gaps, guiding selection of optimal read lengths for complete genome sequencing.

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Last Updated: Jun 10, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Amplicon Sequencing using the Long-Read Sequencing Technologies

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Next-generation sequencing (NGS) technologies offer cost-effective options with short reads.
Uncertainty exists regarding the utility of short reads for de novo assembly of complete prokaryotic genomes due to repeat resolution challenges.

Purpose of the Study:

To develop and test a technique for predicting unresolvable repeats and assembly gaps based on read length.
To quantitatively assess the performance of various read lengths for prokaryotic genome assembly.

Main Methods:

Developed a repeat assembly model to estimate unresolvable repeats and predict genome gaps.
Applied the technique to 818 prokaryotic genome sequences to evaluate different read lengths.

Main Results:

A method was developed to estimate genome gaps for any read length.
Approximately 50% of analyzed prokaryotic genomes can be reconstructed with <96 gaps using 150nt unpaired reads.
Significant variation exists; some genomes require longer reads for near-contiguity.

Conclusions:

Sequencing strategies should be tailored to specific prokaryotic organisms due to genomic diversity.
The study provides a resource for selecting appropriate read lengths for complete genome assembly.