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Fragman: an R package for fragment analysis.

Giovanny Covarrubias-Pazaran1, Luis Diaz-Garcia2,3, Brandon Schlautman2

  • 1Department of Horticulture, University of Wisconsin, Madison, WI, USA. cova_ruber@live.com.mx.

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|April 22, 2016
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Summary

Fragman is a new R package for automated DNA fragment analysis, offering a platform-independent solution for genetic studies. It provides high-throughput capabilities for microsatellite analysis and data conversion for various genetic software.

Keywords:
Fragment analysisGenetic markersLeast squaresOpen source softwareR package

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Area of Science:

  • Genetics
  • Bioinformatics

Background:

  • DNA fragment length determination is crucial for genetic studies like mutation detection and mapping.
  • Existing software often lacks platform independence and high-throughput capabilities.

Purpose of the Study:

  • To introduce Fragman, a free, platform-independent R package for automated DNA fragment analysis.
  • To provide tools for analyzing diversity panels and biparental populations.

Main Methods:

  • Fragman analyzes DNA fragment lengths from Applied Biosystems (ABI) platforms.
  • It supports manual or automatic scoring using panels or bins.
  • Includes tools for data conversion to GenAlEx, JoinMap, and OneMap formats.

Main Results:

  • Fragman enables automatic scoring of DNA fragment lengths for genetic diversity and linkage map generation.
  • Demonstrated with microsatellite marker analysis in cranberry (Vaccinium macrocarpon) genotypes.
  • Offers easy plotting and multiplexing capabilities.

Conclusions:

  • Fragman is a valuable tool for genetic analysis, providing automation for high-throughput experiments.
  • It yields results comparable to existing software with added advantages.
  • Leverages the power of R for efficient genetic data processing.