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Related Concept Videos

Genomics02:02

Genomics

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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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...
Next-generation Sequencing03:00

Next-generation Sequencing

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.
Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
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,...

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Related Experiment Video

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Genotyping in the cloud with Crossbow.

James Gurtowski1, Michael C Schatz1, Ben Langmead2

  • 1Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

Current Protocols in Bioinformatics
|September 6, 2012
PubMed
Summary

Crossbow is a scalable tool for identifying single nucleotide polymorphisms (SNPs) from sequencing data using cloud computing. It analyzes billions of short reads per hour on a Hadoop cluster.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing generates vast amounts of data.
  • Identifying genetic variations like SNPs is crucial for genomic research.
  • Existing tools may lack scalability or ease of use for large datasets.

Purpose of the Study:

  • To introduce Crossbow, a novel cloud computing tool for automated SNP identification.
  • To demonstrate the scalability and efficiency of Crossbow for analyzing short-read resequencing data.
  • To provide practical examples of Crossbow's application in different computing environments.

Main Methods:

  • Crossbow utilizes Apache Hadoop and the MapReduce framework for distributed computing.
  • It integrates Bowtie for read alignment and SOAPsnp for variant calling.
  • The tool supports analysis on Hadoop clusters, single computers, and cloud platforms like Amazon EMR.

Main Results:

  • Crossbow achieves high-throughput analysis, processing approximately one billion short reads per hour.
  • The tool demonstrates scalability on a 320-core Hadoop cluster.
  • Successful identification of SNPs from high-coverage resequencing data was achieved.

Conclusions:

  • Crossbow offers a scalable, portable, and automated solution for SNP discovery.
  • Its cloud-based architecture facilitates efficient analysis of large-scale genomic data.
  • Crossbow provides a flexible platform for variant identification across diverse computational setups.