OMWare: a tool for efficient assembly of genome-wide physical maps.

Aaron R Sharp,Joshua A Udall

doi:10.1186/s12859-016-1099-1

Abstract

BackgroundPhysical 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.ResultsHere 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.ConclusionsResulting assemblies had variable qualities. Although highly accurate assemblies were found, contiguity and internal consistency metrics were poor predictors of accuracy.

Highlights

Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing
The ability to answer certain genomic questions is dependent on read length, and in some cases, the most commonly available read lengths are shorter than what is required [2]
High molecular weight (HMW) DNA sequencing by PacBio has had success producing significantly longer read lengths than many other technologies [4], but even their impressive maximum read length, 40 kb, may still be too short to answer some questions regarding genomic structural variants [5]

Summary

Introduction

Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. The ability to answer certain genomic questions is dependent on read length, and in some cases, the most commonly available read lengths are shorter than what is required [2]. High molecular weight (HMW) DNA sequencing by PacBio has had success producing significantly longer read lengths than many other technologies [4], but even their impressive maximum read length, 40 kb, may still be too short to answer some questions regarding genomic structural variants [5]. Until sequencing technologies are able to characterize longer molecules, alternative methods for HMW DNA assembly are required. Restriction fragment length analysis has long been a preferred method for analyzing longer DNA molecules [6,7,8]

Methods

Results

Conclusion