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selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.

Zachary A Szpiech1, Ryan D Hernandez2

  • 1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco zachary.szpiech@ucsf.edu.

Molecular Biology and Evolution
|July 13, 2014
PubMed
Summary
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We developed selscan, a fast software tool for detecting natural selection in large genomic datasets. This efficient application speeds up haplotype-based scans, aiding in the identification of positive selection across populations.

Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Haplotype-based scans are crucial for identifying recent or ongoing positive selection in genomes.
  • Increasingly large genomic datasets necessitate faster and more efficient computational tools for selection scans.

Discussion:

  • selscan offers a multithreaded implementation of Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population EHH (XPEHH).
  • The software is designed for efficiency, processing large datasets significantly faster than existing methods.
  • It accepts phased genotypes in various formats, enhancing its general usability.

Key Insights:

  • selscan demonstrates substantial speed improvements, processing extensive genomic data in minutes rather than hours.
  • The tool provides accurate results on both simulated and real genomic data.

Related Experiment Videos

  • Demonstrated speedup on chromosome 22 data highlights its performance capabilities.

    • Outlook:

    • selscan is poised to become a valuable tool for researchers studying adaptation and genetic variation.
    • Its efficiency will facilitate large-scale genomic analyses, enabling deeper insights into evolutionary processes.
    • Availability of source code and binaries across multiple platforms promotes widespread adoption and use.