Introduction

Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensitive to input parameters, which describe noise inherent in the data collection process. One possible way to determine the parameter values that best describe a dataset is by trial and error.Here we present OMWare, a tool that efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii. The assemblies were generated using various input parameter values, and were completed more efficiently by re-using compatible intermediate results. These assemblies were assayed for contiguity, internal consistency, and accuracy.Resulting assemblies had variable qualities. Although highly accurate assemblies were found, contiguity and internal consistency metrics were poor predictors of accuracy.

Publications

  1. OMWare: a tool for efficient assembly of genome-wide physical maps.
    Cite this
    Sharp AR, Udall JA, 2016-07-01 - BMC bioinformatics

Credits

  1. Aaron R Sharp
    Developer

    College of Life Sciences, Brigham Young University, United States of America

  2. Joshua A Udall
    Investigator

    College of Life Sciences, Brigham Young University, United States of America

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Summary
AccessionBT000212
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJoshua A Udall