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

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

19.4K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
19.4K
Next-generation Sequencing03:00

Next-generation Sequencing

101.9K
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....
101.9K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.3K
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...
7.3K
Sanger Sequencing01:57

Sanger Sequencing

780.2K
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...
780.2K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

20.1K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
20.1K

You might also read

Related Articles

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

Sort by
Same author

Antibiotic growth promoter and phytogenic feed additive consistently alter microbial community structure in chicken cecum.

Frontiers in microbiology·2026
Same author

Condition-dependent amorphous protein agglomerates control cytoplasmic rheology.

Molecular cell·2026
Same author

Gap Analysis of Metabolic Conversions of Off-Flavors and Antinutrients in Plant-Based Substrates.

Comprehensive reviews in food science and food safety·2026
Same author

Oral-heart axis from pregnancy and postpartum: maternal oral microbiota relates with cardiac reverse remodeling.

Journal of oral microbiology·2026
Same author

Cancer-associated fibroblast signature and SMAD4 mutation in resistance to adjuvant chemotherapy in stage III colon cancer patients.

European journal of cancer (Oxford, England : 1990)·2026
Same author

Beyond olfaction: New insights into human odorant binding proteins.

Protein science : a publication of the Protein Society·2026
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: Apr 14, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.7K

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

Ali May1, Sanne Abeln2, Mark J Buijs3

  • 1Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands.

Nucleic Acids Research
|April 17, 2015
PubMed
Summary
This summary is machine-generated.

NGS-eval assesses sequencing quality by analyzing microbial genetic marker (MGM) reads against known references. This tool helps estimate error rates and detect variants in sequencing data, crucial for metagenomics.

More Related Videos

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

17.5K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.3K

Related Experiment Videos

Last Updated: Apr 14, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.7K
Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

17.5K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.3K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Massively parallel sequencing of microbial genetic markers (MGMs) is vital for determining species composition in diverse environments.
  • Mock samples with known compositions are essential for evaluating sequencing quality and identifying novel sequence variants.
  • Accurate sequencing error rate estimation relies on correct reference sequences, which can be challenging to select from databases.

Purpose of the Study:

  • To introduce NGS-eval, a computational tool for analyzing MGM reads from mock samples.
  • To explore differences between sequencing reads and their references.
  • To estimate sequencing error rates and detect sequence variants using NGS-eval.

Main Methods:

  • NGS-eval maps sequencing reads to reference sequences.
  • The tool calculates and visualizes various types of sequencing errors.
  • Demonstration of variant detection and error analysis using Illumina MiSeq reads from a mock community.

Main Results:

  • NGS-eval effectively analyzes Illumina MiSeq reads for variant detection and error profiling.
  • The tool aids in understanding the accuracy of sequencing runs for MGM analysis.
  • Demonstrated capability to estimate sequencing error rates and identify sequence variants.

Conclusions:

  • NGS-eval provides a robust method for evaluating sequencing quality and error rates in MGM data.
  • The tool is applicable to various MGM-based sequencing datasets beyond metagenomics.
  • NGS-eval is accessible online for researchers to assess their sequencing data.