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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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SV-Pop: population-based structural variant analysis and visualization.

Matt Ravenhall1, Susana Campino2, Taane G Clark2,3

  • 1Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK. matt.ravenhall@lshtm.ac.uk.

BMC Bioinformatics
|March 15, 2019
PubMed
Summary
This summary is machine-generated.

We developed SV-Pop, a tool for analyzing genetic structural variations (SVs). This pipeline facilitates high-throughput analysis and visualization of SVs across multiple populations, improving genetic studies.

Keywords:
AnalyticsBioinformaticsPopulation genomicsPythonRShinyStructural variation

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Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Genetic structural variations (SVs) significantly influence phenotypes but are often understudied compared to single nucleotide polymorphisms (SNPs).
  • SVs play a crucial role in biological outcomes and disease, yet their analysis is challenging.
  • Large-scale genetic studies frequently overlook SVs, limiting comprehensive genomic insights.

Purpose of the Study:

  • To develop a high-throughput analytical pipeline and visualization tool for structural variation analysis.
  • To enable efficient integration of multi-population data for SV studies.
  • To facilitate the downstream analysis and visualization of structural variants.

Main Methods:

  • Development of an analytical pipeline named SV-Pop.
  • Creation of a visualization tool integrated within the SV-Pop pipeline.
  • Application of the SV-Pop pipeline to a large, multi-population Plasmodium falciparum dataset.

Main Results:

  • SV-Pop successfully facilitates high-throughput analysis of structural variation.
  • The utility of SV-Pop was demonstrated using a large Plasmodium falciparum dataset.
  • The pipeline enables straightforward integration of multi-population analysis, concordance metrics, and selection signals.

Conclusions:

  • SV-Pop is a valuable tool for post-discovery analysis and visualization of structural variants.
  • The pipeline simplifies the integration of multi-population SV data.
  • SV-Pop aids in identifying concordance metrics and signals of selection across diverse populations.