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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Sanger Sequencing01:57

Sanger Sequencing

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...
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...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

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Related Experiment Video

Updated: Jun 10, 2026

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

Structural variant calling using Sniffles2.

Luis F Paulin1, Hermann Romanek1, Farhang Jaryani1,2,3

  • 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.

Nature Protocols
|June 8, 2026
PubMed
Summary
This summary is machine-generated.

Sniffles2 software reliably detects structural variants (SVs) from long-read sequencing data. This protocol details its use for germline, mosaic, and joint SV calling in various applications, offering high precision and speed.

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Last Updated: Jun 10, 2026

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

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

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

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Structural variants (SVs) are common genomic alterations with significant roles in evolution, disease, and gene regulation.
  • Accurate SV detection is crucial for understanding genetic variation and its impact.

Purpose of the Study:

  • To provide a comprehensive protocol for utilizing Sniffles2 (v2.6.3) for precise identification of germline and mosaic structural variants.
  • To detail SV joint calling capabilities for tumor/normal and family trio analyses, scalable to population studies.

Main Methods:

  • Utilizing Sniffles2 software for structural variant detection from long-read sequencing data.
  • Implementing protocols for germline, mosaic (5-22% VAF), and joint SV calling.
  • Benchmarking Sniffles2 against existing tools for precision and speed.

Main Results:

  • Sniffles2 demonstrates high precision in detecting structural variants across various types (deletions, duplications, insertions, inversions, translocations).
  • The tool accurately identifies low-variant allele fraction mosaic SVs.
  • Sniffles2 achieves rapid SV calling, processing a 40x human genome in approximately 34 CPU minutes.

Conclusions:

  • Sniffles2 is a fast, precise, and user-friendly tool for comprehensive structural variant analysis using long-read sequencing.
  • The detailed protocol enables accurate germline and mosaic SV detection and joint calling for diverse research applications.