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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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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Next-generation Sequencing03:00

Next-generation Sequencing

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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....
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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RNA-seq03:21

RNA-seq

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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. 
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Sanger Sequencing01:57

Sanger Sequencing

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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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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
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Related Experiment Video

Updated: Jul 18, 2025

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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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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Comparing assembly strategies for third-generation sequencing technologies across different genomes.

Elena Espinosa1, Rocio Bautista2, Ivan Fernandez3

  • 1Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain.

Genomics
|August 20, 2023
PubMed
Summary
This summary is machine-generated.

Long-read sequencing, including PacBio HiFi and Oxford Nanopore (ONT), improves genome assembly. High-fidelity ONT data, combined with HiFi or short reads, significantly enhances assembly correctness and haplotype construction.

Keywords:
Genome assemblyHiFiHybrid assemblyONTPacBio

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Related Experiment Videos

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

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Long-read sequencing technologies like Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) have advanced genome assembly.
  • Despite improvements, de novo whole-genome assembly faces challenges in computational cost and result quality.
  • Emerging tools and improving accuracy necessitate careful selection of sequencing platforms, depth, and assembly strategies.

Purpose of the Study:

  • To evaluate primary genome assembly reconstruction using hybrid and non-hybrid pipelines.
  • To compare the performance of different long-read sequencing technologies (PacBio HiFi and ONT) in genome assembly.
  • To identify optimal strategies for high-quality genome assembly.

Main Methods:

  • Evaluation of hybrid and non-hybrid assembly pipelines.
  • Comparative analysis of PacBio HiFi and Oxford Nanopore (ONT) long-read data.
  • Assessment of assembly correctness and haplotype construction capabilities.

Main Results:

  • PacBio HiFi long-reads are crucial for haplotype construction compared to ONT reads.
  • High-fidelity ONT datasets significantly improve assembly correctness.
  • Combining high-fidelity ONT data with PacBio HiFi or short reads further enhances assembly quality.

Conclusions:

  • The choice of sequencing platform, depth, and assembly tools is critical for high-quality genome assembly.
  • High-fidelity long-read data, particularly from ONT, offers substantial improvements in assembly correctness.
  • Hybrid approaches combining different data types yield superior genome assembly results.