title: OMWare: a tool for efficient assembly of genome-wide physical maps.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  Resulting assemblies had variable qualities. Although highly accurate assemblies were found, contiguity and internal consistency metrics were poor predictors of accuracy.
authors.affiliation: College of Life Sciences, Brigham Young University, Provo, UT, 84602-2400, USA. sharp.aaron.r@gmail.com.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Sharp
authors.affiliation: College of Life Sciences, Brigham Young University, Provo, UT, 84602-2400, USA.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
mesh_terms: D000068598:Data Accuracy; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D020161:Physical Chromosome Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software