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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...

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...

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Related Experiment Video

Updated: Mar 20, 2026

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

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.

Valerio Bianchi¹, Arnaud Ceol¹, Alessandro G E Ogier²

¹Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia Milano, Italy.

Frontiers in Genetics

|May 21, 2016

Summary

Managing next-generation sequencing (NGS) data is challenging for labs. HTS-flow offers a solution by addressing data management, analysis traceability, and user accessibility for complex biological datasets.

Keywords:

epigenomics genomics high-throughput sequencing laboratory information management system workflow management system

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

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Last Updated: Mar 20, 2026

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

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

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Next-generation sequencing (NGS) generates vast amounts of data, transforming biological research.
Many research groups lack the IT and quantitative expertise to manage and analyze NGS data effectively.
Challenges in data management can hinder the full utilization of NGS technologies.

Purpose of the Study:

To identify key challenges in managing and analyzing NGS data for research groups.
To propose solutions and tools for effective NGS data handling and analysis.
To introduce HTS-flow as a workflow management system designed to address these challenges.

Main Methods:

Identification of five critical issues in NGS data management and analysis.
Evaluation of existing tools in the context of these identified issues.
Development and introduction of the HTS-flow workflow management system.

Main Results:

Five key issues identified: LIMS adoption, data flow monitoring, analysis traceability, GUI for users, and metadata standardization.
HTS-flow is presented as a system addressing these issues.
HTS-flow integrates with LIMS, provides a GUI, ensures traceability, and standardizes data output.

Conclusions:

Effective management of NGS data requires careful consideration of laboratory management systems, data flow, traceability, user interface, and metadata.
HTS-flow provides a comprehensive solution for managing NGS data workflows, enhancing accessibility and reliability for research groups.