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

Next-generation Sequencing03:00

Next-generation Sequencing

88.0K
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....
88.0K
Sanger Sequencing01:57

Sanger Sequencing

801.2K
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...
801.2K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

11.6K
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%...
11.6K
RNA-seq03:21

RNA-seq

9.5K
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...
9.5K
Improving Translational Accuracy02:07

Improving Translational Accuracy

11.6K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.6K
Improving Translational Accuracy02:07

Improving Translational Accuracy

2.7K
2.7K

You might also read

Related Articles

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

Sort by
Same author

Reduced Soluble Ubiquilin2 in Amyotrophic Lateral Sclerosis Carrying Ubiquilin2 (P494L) Mutation: Clinicopathological and Biochemical Evidence From an Autopsy Case.

Neuropathology and applied neurobiology·2026
Same author

Accuracy in Percent Body Fat from Skinfold Prediction Equations Vary Among Young, Middle-Age, and Older Male and Female Caucasians.

The British journal of nutrition·2026
Same author

A translocation-mediated duplication of the distal region of chromosome 5A reduced the culm length in a gamma-irradiated wheat mutant.

Molecular breeding : new strategies in plant improvement·2026
Same author

Fine-tuning quantitative agronomic traits by manipulating gene copy number in rice.

The New phytologist·2026
Same author

Whole-genome sequencing reveals a possible molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro.

PLoS genetics·2026
Same author

Retrospective Study on the Effects of Intensive Speech Therapy Combined with Two Courses of High-Frequency rTMS on Language Function in Patients with Aphasia.

NeuroRehabilitation·2026

Related Experiment Video

Updated: May 7, 2026

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

15.0K

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

Shunichi Kosugi1, Satoshi Natsume, Kentaro Yoshida

  • 1Iwate Biotechnology Research Center, Kitakami, Iwate, Japan ; Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.

Plos One
|October 12, 2013
PubMed
Summary
This summary is machine-generated.

Coval software enhances DNA polymorphism identification by improving short read alignments and reducing errors. This leads to more accurate single nucleotide polymorphism (SNP) and indel calling in next-generation sequencing data.

More Related Videos

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

36.1K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

16.6K

Related Experiment Videos

Last Updated: May 7, 2026

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

15.0K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

36.1K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

16.6K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) presents challenges in accurate DNA polymorphism identification due to sequencing errors and read mapping inaccuracies.
  • Existing short read aligners and variant callers are limited by these inherent problems.

Purpose of the Study:

  • To develop Coval software for improving the quality of short read alignments in NGS data.
  • To minimize spurious alignments and enhance the accuracy of DNA variant identification.

Main Methods:

  • Coval filters mismatched reads post-realignment and employs error correction based on base quality and allele frequency.
  • The software utilizes a strategy to minimize spurious alignment of short reads.
  • Error correction is applied to individual or pooled samples.

Main Results:

  • Coval demonstrated utility on simulated genomes and experimental short-read data from rice, nematode, and mouse.
  • The software effectively eliminated a significant number of incorrectly mapped reads in targeted alignments.
  • Coval improved the quality of short-read sequence alignments.

Conclusions:

  • Coval significantly enhances the quality of short-read alignments.
  • The software increases the accuracy of single nucleotide polymorphism (SNP) and insertion-deletion (indel) identification.
  • Coval is a valuable tool for improving variant calling in NGS data analysis.