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

100.8K
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....
100.8K
Sanger Sequencing01:57

Sanger Sequencing

778.0K
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...
778.0K
RNA-seq03:21

RNA-seq

12.4K
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...
12.4K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

19.2K
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%...
19.2K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.5K
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.
21.5K
Genomics02:02

Genomics

41.7K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
41.7K

You might also read

Related Articles

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

Sort by
Same author

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.

bioRxiv : the preprint server for biology·2026
Same author

The complete genome of the KOLF2.1J reference iPSC line.

bioRxiv : the preprint server for biology·2026
Same author

A complete diploid human genome benchmark for personalized genomics.

bioRxiv : the preprint server for biology·2025
Same author

Random forest classifiers trained on simulated data enable accurate short read-based genotyping of structural variants in the alpha globin region at Chr16p13.3.

bioRxiv : the preprint server for biology·2023
Same author

The complete sequence of a human Y chromosome.

Nature·2023
Same author

Long-read mapping to repetitive reference sequences using Winnowmap2.

Nature methods·2022
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Mar 23, 2026

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

35.0K

Variant Calling From Next Generation Sequence Data.

Nancy F Hansen1

  • 1National Human Genome Research Institute, Rockville, MD, USA.

Methods in Molecular Biology (Clifton, N.J.)
|March 24, 2016
PubMed
Summary
This summary is machine-generated.

This study presents a free software workflow for analyzing next-generation sequencing data to identify genetic variants associated with diseases. The methods enable accurate variant calling, annotation, and filtering for research.

Keywords:
AnnotationGenotypingNext generation sequencingVariant detectionWhole exome

More Related Videos

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

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.2K
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

Related Experiment Videos

Last Updated: Mar 23, 2026

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

35.0K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.2K
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

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Next-generation sequencing (NGS) has revolutionized the identification of genetic variants.
  • Understanding small sequence variants is crucial for deciphering disease mechanisms.

Purpose of the Study:

  • To describe a freely available software pipeline for analyzing NGS data.
  • To detail a workflow for variant calling, annotation, and filtering.

Main Methods:

  • Read alignment using novoalign.
  • Duplicate removal with samtools or bamUtils.
  • Variant detection using Freebayes or bam2mpg.
  • Variant annotation with ANNOVAR.
  • Variant visualization and filtering with VarSifter.

Main Results:

  • A comprehensive workflow for small sequence variant analysis from NGS data is presented.
  • The workflow integrates multiple open-source tools for efficient processing.

Conclusions:

  • Freely available software can be effectively used to call, annotate, and filter small sequence variants from NGS data.
  • This approach facilitates the study of molecular causes of diseases.