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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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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.
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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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Updated: Jul 9, 2025

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
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Improved sequence mapping using a complete reference genome and lift-over.

Nae-Chyun Chen1, Luis F Paulin2, Fritz J Sedlazeck2,3

  • 1Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. cnaechy1@jhu.edu.

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|November 30, 2023
PubMed
Summary
This summary is machine-generated.

levioSAM2 enables fast and accurate genome assembly lift-over between references. Aligning reads to high-quality assemblies like T2T-CHM13 and lifting to older references improves variant calling accuracy, especially for medically relevant genes.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Complete genome assemblies, such as telomere-to-telomere (T2T), offer enhanced analyses and variant discovery.
  • Essential genomic resources are often tied to older reference genomes, necessitating methods for cross-reference compatibility.

Purpose of the Study:

  • To introduce levioSAM2, a novel method for efficient and precise lift-over of genomic features and read alignments between different genome assemblies.
  • To demonstrate the utility of levioSAM2 in improving variant calling accuracy by leveraging high-quality T2T references.

Main Methods:

  • Development and application of levioSAM2, a whole-genome map-based lift-over tool.
  • Alignment of short and long sequencing reads to both high-quality T2T-CHM13 and older GRC references.
  • Comparative analysis of variant calling accuracy between levioSAM2-processed data and standard GRC-based mapping.

Main Results:

  • levioSAM2 provides fast and accurate lift-over between diverse genome assemblies.
  • Aligning reads to T2T-CHM13 and lifting to GRC reference improves variant call accuracy compared to direct GRC mapping.
  • Significant reduction in small and structural variant calling errors observed, particularly for complex, medically relevant genes with lower quality GRC references.

Conclusions:

  • levioSAM2 facilitates the translation of genomic data between reference assemblies.
  • Utilizing high-quality T2T references with levioSAM2 enhances the accuracy of variant detection on older, widely used references.
  • The method offers substantial improvements for genomic analyses, especially in regions of biological and medical significance.