OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps.

ABSTRACT:

Background

Optical 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 information over much longer (up to 1 Mb) reads. 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.

Findings

We present a new method, OMMA, 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 nu

SUBMITTER: Leung AK 

PROVIDER: S-EPMC6615982 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature