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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.

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Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Genomics

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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: Jun 19, 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

inGAP: an integrated next-generation genome analysis pipeline.

Ji Qi¹, Fangqing Zhao, Anne Buboltz

¹Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA.

Bioinformatics (Oxford, England)

|November 3, 2009

Summary

A new pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), accurately detects genetic variations like single nucleotide polymorphisms (SNPs) and indels. This tool aids in bacterial genome assembly and comparative genomics.

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Last Updated: Jun 19, 2026

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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

Area of Science:

Genomics
Bioinformatics

Background:

High-throughput sequencing generates vast amounts of genomic data.
Accurate variant detection is crucial for understanding genetic diversity and disease.

Purpose of the Study:

To develop a novel bioinformatics pipeline for detecting genetic variations.
To provide a robust tool for analyzing next-generation sequencing data.

Main Methods:

Developed the Integrative Next-generation Genome Analysis Pipeline (inGAP).
Employed a Bayesian principle for variant detection.
Utilized comparative analysis against a reference genome.

Main Results:

Achieved 97% accuracy in single nucleotide polymorphism (SNP) detection.
Achieved 94% accuracy in insertion/deletion (indel) detection.
Demonstrated applicability to both Roche/454 and Illumina sequencing reads.

Conclusions:

inGAP is an accurate and versatile pipeline for variant discovery.
The pipeline supports multiple genome comparisons and bacterial genome assembly.
inGAP offers a graphical editor for variant evaluation.