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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,...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...

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Related Experiment Video

Updated: Jun 18, 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

Searching for SNPs with cloud computing.

Ben Langmead1, Michael C Schatz, Jimmy Lin

  • 1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA. blangmea@jhsph.edu

Genome Biology
|November 26, 2009
PubMed
Summary
This summary is machine-generated.

Accelerating DNA sequencing analysis, Crossbow software integrates alignment and SNP calling. This cloud-based tool significantly reduces processing time and cost for large-scale genomic data.

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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

Related Experiment Videos

Last Updated: Jun 18, 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

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

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • DNA sequencing technologies generate vast amounts of data, outpacing traditional computational analysis speeds.
  • Accurate and rapid alignment and single nucleotide polymorphism (SNP) calling are essential for genomic research and clinical applications.

Purpose of the Study:

  • To develop and evaluate Crossbow, a novel cloud-computing software tool designed to accelerate DNA sequencing data analysis.
  • To combine established bioinformatics tools, Bowtie for alignment and SOAPsnp for SNP calling, into an integrated and parallelized workflow.

Main Methods:

  • Crossbow utilizes Hadoop for parallel processing, integrating the Bowtie aligner and SOAPsnp variant caller.
  • The software was tested on a 38-fold coverage dataset of the human genome.
  • Cloud computing resources were employed, specifically a 320-CPU cluster.

Main Results:

  • Crossbow successfully analyzed 38-fold human genome coverage data in approximately three hours.
  • The analysis was performed using a 320-CPU cluster, demonstrating efficient parallelization.
  • The computational cost for the analysis was approximately $85, highlighting cost-effectiveness.

Conclusions:

  • Crossbow offers a significant acceleration for essential DNA sequencing analysis tasks like alignment and SNP calling.
  • The cloud-based, parallelized approach of Crossbow provides a scalable and cost-effective solution for large-scale genomic data processing.