Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

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.
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...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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
The...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Publisher Correction: Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.

Nature structural & molecular biology·2026
Same author

3D Volumetric-Based resection modeling to optimize reconstructive outcomes for ablative oral cavity defects.

Oral oncology·2026
Same author

Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes.

bioRxiv : the preprint server for biology·2026
Same author

Preoperative Neutrophil-to-Lymphocyte Ratio Predicts Recurrence in HPV-Associated Oropharyngeal Cancer After Transoral Robotic Surgery.

Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery·2026
Same author

Saturation Genome Editing reveals the functional impact of RAD51D <i>and</i> XRCC2 variants.

bioRxiv : the preprint server for biology·2026
Same author

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos.

bioRxiv : the preprint server for biology·2026
Same journal

A human-specific genetic modifier reconfigures large-scale cortical network dynamics underlying behavioral performance.

bioRxiv : the preprint server for biology·2026
Same journal

<i>Staphylococcus aureus</i> uses a eukaryotic-like uridyltransferase to make UDP-GlcNAc for cell wall synthesis.

bioRxiv : the preprint server for biology·2026
Same journal

Dynamic redistribution of eIF4F controls cap-dependent translation initiation.

bioRxiv : the preprint server for biology·2026
Same journal

When does additional information improve accuracy of RNA secondary structure prediction?

bioRxiv : the preprint server for biology·2026
Same journal

Normative brain-state trajectories reveal deviation from healthy aging in Alzheimer's disease.

bioRxiv : the preprint server for biology·2026
Same journal

Noradrenergic infraslow rhythm during sleep is the critical link between heart-rate dynamics and memory consolidation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Jul 4, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Short-Read Sequencing Benchmarking with Donor-Specific Assemblies.

Sean R McGee, Joshua D Smith, Christian D Frazar

    Biorxiv : the Preprint Server for Biology
    |July 3, 2026
    PubMed
    Summary
    This summary is machine-generated.

    Benchmarking short-read DNA sequencing platforms reveals significant differences in error profiles. Donor-specific references are crucial for accurate sequencing error measurement and platform comparison, aiding rare variant detection.

    More Related Videos

    Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
    10:41

    Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

    Published on: May 9, 2017

    Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
    08:35

    Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

    Published on: June 24, 2021

    Related Experiment Videos

    Last Updated: Jul 4, 2026

    Novel Sequence Discovery by Subtractive Genomics
    09:40

    Novel Sequence Discovery by Subtractive Genomics

    Published on: January 25, 2019

    Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
    10:41

    Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

    Published on: May 9, 2017

    Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
    08:35

    Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

    Published on: June 24, 2021

    Area of Science:

    • Genomics
    • Bioinformatics
    • Sequencing Technology

    Background:

    • High-throughput short-read sequencing is vital in genomics.
    • Platform expansion necessitates standardized benchmarking.
    • Conventional methods confound sequencing errors with biological variation and reference bias.

    Purpose of the Study:

    • To benchmark short-read sequencing chemistries and platforms.
    • To develop a standardized method for isolating platform-intrinsic sequencing errors.
    • To compare platform performance using characterized samples and donor-specific references.

    Main Methods:

    • Benchmarking nine short-read chemistries across seven DNA sequencers.
    • Utilizing characterized samples HG002 and COLO829BL.
    • Employing donor-specific assemblies for sample-matched genomic reference comparisons.

    Main Results:

    • Identified substantial differences in substitution, indel, read-position, and sequence-context error profiles.
    • Element AVITI UltraQ and Roche SBX-D showed lowest substitution errors; Ultima and Roche chemistries had strongest indel biases.
    • Observed platform-specific effects in low-complexity regions and trinucleotide contexts, impacting rare variant detection.
    • Demonstrated the necessity of donor-specific references for unbiased base-quality recalibration and cross-platform comparison.

    Conclusions:

    • Donor-specific assembly-based benchmarking offers a robust framework for measuring true short-read sequencing errors.
    • Established a comprehensive reference for sequencing platform performance.
    • Authentic error profiles can guide platform selection, quality filtering, and improve rare somatic variation detection.