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Numericware i: Identical by State Matrix Calculator.

Bongsong Kim1, William D Beavis1

  • 1Department of Agronomy, Iowa State University, Ames, IA, USA.

Evolutionary Bioinformatics Online
|May 5, 2017
PubMed
Summary

Numericware i software efficiently computes the identical by state (IBS) matrix for large genotypic datasets. It overcomes memory and processing challenges using multithreading and forward chopping, enabling analysis on standard computers.

Keywords:
Forward choppingGenetic relationship matrixIdentical by state matrixMultithreadingNumericware i

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Calculating an identical by state (IBS) matrix from large genotypic datasets is computationally intensive, requiring significant memory and processing time.
  • Existing software may struggle with high-dimensional datasets, limiting scalability and accessibility for researchers.

Purpose of the Study:

  • To introduce Numericware i, a novel software designed for efficient IBS matrix computation.
  • To address the computational challenges associated with large-scale genotypic data analysis.
  • To provide a scalable and accessible tool for genetic relationship matrix calculation.

Main Methods:

  • Implementation of multithreading to enable concurrent processing across multiple CPU cores.
  • Development of a forward chopping algorithm to divide large datasets into manageable subsets, mitigating memory limitations.
  • Comparative analysis of Numericware i against established software (SPAGeDi, TASSEL) using identical genotypic datasets.

Main Results:

  • Numericware i successfully computed IBS matrices for high-dimensional datasets where other software failed.
  • The software demonstrated high correlation (.9972) with TASSEL and significantly outperformed SPAGeDi in terms of correlation (.0505).
  • Numericware i efficiently processed a dataset of 500 entities by 10,000,000 SNPs in 382 minutes on a standard computer.

Conclusions:

  • Numericware i offers an efficient and scalable solution for IBS matrix computation from large genotypic datasets.
  • The software's algorithmic innovations make complex genetic analyses feasible on standard hardware.
  • Numericware i is freely available, promoting wider accessibility in genetic research.