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Related Concept Videos

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...

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...

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

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...

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.

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Related Experiment Video

Updated: Jun 10, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

SEWAL: an open-source platform for next-generation sequence analysis and visualization.

Jason N Pitt¹, Indika Rajapakse, Adrian R Ferré-D'Amaré

¹Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. jpitt@fhcrc.org

Nucleic Acids Research

|August 10, 2010

Summary

This summary is machine-generated.

This study introduces new open-source software for analyzing large next-generation DNA sequencing datasets. It efficiently enumerates unique sequences and visualizes data, aiding genetic analysis and doped selections.

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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

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Last Updated: Jun 10, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

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:

Bioinformatics
Computational Biology
Genomics

Background:

Next-generation DNA sequencing generates vast datasets, posing computational and analytical challenges for in vitro genetic analysis.
Efficiently processing and analyzing these large-scale sequencing data is crucial for advancing functional nucleic acid research.

Purpose of the Study:

To present an open-source software package for the rapid enumeration and analysis of unique sequences from high-throughput sequencing runs.
To provide tools for visualizing complex sequencing data and performing specialized analyses for applications like doped selections.

Main Methods:

Implementation of a locality-sensitive hashing algorithm for enumerating unique sequences in massive datasets (approx. 10^8 sequences).
Development of quasilinear time processing capabilities for entire Illumina lanes (approx. 10^7 sequences) on standard desktop computers.
Integration of functions for mutation frequency analysis, information content calculation, multivariate statistics (PCA), and sequence comparison.

Main Results:

The software enables quasilinear time processing of entire Illumina lanes in minutes.
Generated three-dimensional scatter plots for visual analysis, analogous to adaptive landscapes.
Provided specialized functions for doped selections, mutation analysis, and cross-dataset comparisons.

Conclusions:

The developed open-source software package offers an efficient solution for handling and analyzing large-scale next-generation sequencing data.
The tool facilitates advanced genetic analysis, data visualization, and specific applications like doped selections, making complex data more accessible.