OMWare: a tool for efficient assembly of genome-wide physical maps. Issue 7 (July 2016)

• Record Type: Journal Article
• Authors: Sharp, Aaron; Udall, Joshua
• Is Part Of: BMC bioinformatics. Volume 17:Issue 7(2016)
• Page Start: 511
• Page End: 516
• Publication Date: 2016-07
• Subjects: Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-016-1099-1
• Languages: English
• ISSNs: 1471-2105

Abstract

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 405de novo map assemblies of a single datasets collected from the cotton speciesGossypium 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.