OMMA Enables Population-Scale Analysis of Complex Genomic Features and Phylogenomic Relationships from Nanochannel-Based Optical Maps
Refereed conference paper presented and published in conference proceedings


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AbstractOptical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing long-range information. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples. Here we present a new method, OMMA (Optical Maps in Multiple Alignment), that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g. multiple haplotypes, copy-number variations, and subtelomeric structures when applying to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identies functional elements across 21 Acinetobacter baumannii strains. With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools
All Author(s) ListAlden K. Leung, Ting-Fung Chan
Name of ConferencePlant and Animal Genome Conference XXVII
Start Date of Conference12/01/2019
End Date of Conference16/01/2019
Place of ConferenceSan Diego
Country/Region of ConferenceUnited States of America
Year2019
LanguagesEnglish-United States

Last updated on 2020-15-05 at 12:42