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Related Concept Videos

Next-generation Sequencing03:00

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 Assembly03:36

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-seq03:21

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 Sequencing01:57

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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Related Experiment Video

Updated: Jun 1, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.

Jose M Blanca1, Laura Pascual, Peio Ziarsolo

  • 1Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia, Spain.

BMC Genomics
|June 4, 2011
PubMed
Summary

Next-generation sequencing (NGS) software, ngs_backbone, analyzes sequence reads and predicts single nucleotide variations (SNVs) with high accuracy. This tool aids researchers by identifying genetic polymorphisms in non-model species, as demonstrated in tomato.

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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

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Published on: August 24, 2017

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) platforms are revolutionizing biotechnological research.
  • High-throughput genotyping and NGS accelerate the discovery of single nucleotide polymorphisms (SNPs) in non-model species.
  • The increasing volume of sequence data necessitates advanced software solutions.

Purpose of the Study:

  • To develop a powerful and user-friendly software application for analyzing NGS data.
  • To address the growing software needs arising from abundant sequence data and polymorphisms.
  • To facilitate the discovery and utilization of SNPs in various species.

Main Methods:

  • Developed ngs_backbone, a parallel pipeline for analyzing diverse sequence reads (Sanger, 454, Illumina, SOLiD).
  • Implemented core analyses including read cleaning, transcriptome assembly/annotation, read mapping, and SNP calling.
  • Validated the software using tomato EST and Illumina reads, mapping them to the SGN tomato transcriptome.

Main Results:

  • ngs_backbone successfully analyzed Sanger and Illumina reads, achieving high transcriptome coverage.
  • Predicted 23,360 single nucleotide variations (SNVs) in tomato.
  • Experimentally validated 76 SNVs, confirming 85% accuracy.

Conclusions:

  • ngs_backbone accurately analyzes NGS data and predicts SNVs.
  • The software provides a valuable resource for researchers and breeders, exemplified by the polymorphic SNVs identified in tomato.
  • The ngs_backbone software and its documentation are freely available under the AGPL license.