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Related Concept Videos

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
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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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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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Evolutionary Relationships through Genome Comparisons02:54

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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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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.
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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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Updated: Jul 19, 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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Benchmarking multi-platform sequencing technologies for human genome assembly.

Jingjing Wang1, Werner Pieter Veldsman1, Xiaodong Fang2

  • 1Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.

Briefings in Bioinformatics
|August 18, 2023
PubMed
Summary
This summary is machine-generated.

Benchmarking human genome assembly strategies reveals PacBio HiFi reads offer optimal accuracy, while Oxford Nanopore provides contiguity. Combining technologies and using hifiasm tool enhances diploid genome assembly quality.

Keywords:
contig polishingdiploid assemblyhuman genome assemblymulti-platform sequencingscaffolding

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Generating a high-quality human reference genome is essential for understanding human biology and genomic variation.
  • Numerous sequencing technologies and computational tools exist for genome assembly, but selecting the optimal strategy remains challenging.
  • Previous efforts have focused on improving haploid and diploid genome assemblies through contig assembly, polishing, scaffolding, and variant phasing.

Purpose of the Study:

  • To benchmark various human genome assembly strategies by combining different sequencing technologies and computational tools.
  • To evaluate the performance of these strategies based on continuity, accuracy, completeness, variant calling, and phasing.
  • To identify the most effective approaches for generating high-quality human genome assemblies.

Main Methods:

  • Benchmarking of genome assembly strategies using PacBio HiFi, Oxford Nanopore, 10x linked-reads, Bionano optical maps, and Hi-C technologies.
  • Utilizing publicly available human samples (NA12878 and NA24385) from the Genome in a Bottle consortium.
  • Comparison of assembly performance metrics including contiguity, accuracy, completeness, variant calling, and phasing.

Main Results:

  • PacBio HiFi long-reads are optimal for generating genome assemblies with low base error rates.
  • Oxford Nanopore long-reads yield the most continuous contigs but may require polishing for improved quality.
  • Hi-C technology is superior for chromosome-level scaffolding, outperforming 10x linked-reads and Bionano optical maps.
  • The hifiasm tool, utilizing PacBio HiFi and Hi-C data, is recommended for human diploid genome assembly.
  • Combining multiple sequencing technologies can further enhance genome assembly quality and completeness.

Conclusions:

  • PacBio HiFi reads are recommended for achieving high accuracy in human genome assemblies.
  • Oxford Nanopore reads, when combined with short-reads for polishing, can improve contiguity and accuracy.
  • Hi-C technology is crucial for chromosome-level scaffolding, enabling more complete genome structures.
  • Future advancements in diploid assemblers will likely integrate long-read technologies and long-range DNA information for high-quality, haplotype-resolved assemblies.