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Related Concept Videos

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.
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.
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...
Evolutionary Relationships through Genome Comparisons02:54

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...
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: May 10, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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GAM-NGS: genomic assemblies merger for next generation sequencing.

Riccardo Vicedomini1, Francesco Vezzi, Simone Scalabrin

  • 1Department of Mathematics and Computer Science, University of Udine, 33100 Udine, Italy. rvicedomini@appliedgenomics.org

BMC Bioinformatics
|July 3, 2013
PubMed
Summary

Genomic Assemblies Merger for Next Generation Sequencing (GAM-NGS) merges multiple genome assemblies to improve contiguity and correctness. This tool efficiently reconciles NGS data, offering a superior alternative to single assemblers.

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Last Updated: May 10, 2026

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) assembly presents challenges, with over 20 assemblers available, each with region-specific strengths and weaknesses.
  • Selecting the best single assembler is difficult due to varying performance across different genomic regions and evaluation metrics.

Purpose of the Study:

  • To develop GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), a tool designed to merge multiple genome assemblies.
  • Enhance the contiguity and correctness of de novo assemblies by combining outputs from different assemblers.

Main Methods:

  • GAM-NGS identifies homologous regions (blocks) between assemblies using read alignments, not global alignment.
  • These blocks are stored in a weighted graph to guide the merging process.
  • The weighted graph facilitates optimal resolution of local assembly errors.

Main Results:

  • Tested on six datasets, GAM-NGS demonstrated its ability to produce improved and reliable sequence sets, validated by reference sequences.
  • The tool is computationally efficient, requiring fewer resources than comparable assembly reconciliation methods.
  • GAM-NGS's unique strategy avoids global alignment, distinguishing it from other reconciliation tools.

Conclusions:

  • GAM-NGS addresses the need for algorithms that enhance de novo assemblies, improving contiguity and correctness.
  • The tool is applicable to all NGS assembly projects, particularly beneficial for multi-library Illumina-based projects.
  • By merging assemblies, GAM-NGS offers a method to improve overall assembly quality and potentially identify superior assemblers.