Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes wou...

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Bibliographic Details
Published in:The Plant cell 2018-01, Vol.30 (1), p.7-14
Main Authors: Udall, Joshua A., Dawe, R. Kelly
Format: Article
Language:English
Subjects:
Assemblies
Assembly
Cardiac arrhythmia
COMMENTARY
Gene mapping
Gene sequencing
Genetic resources
Genomes
Mapping
Nucleotide sequence
Synteny
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Summary:Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.
ISSN:1040-4651
1532-298X
DOI:10.1105/tpc.17.00514