Abstract: Disclosed are methods for detecting spatial proximity relationships between nucleic acid sequences, such as genomic DNA, in a cell. The method includes providing a sample of one or more crosslinked cells comprising nucleic acids; permeabilizing isolated nuclei under conditions that preserve contacts; fragmenting the nucleic acids present in the nuclei; filling in and repairing the ends with at least one labeled nucleotide; joining the filled in end of the fragmented nucleic acids that are in close physical proximity to create one or more end joined nucleic acid fragments having a junction; isolating the one or more end joined nucleic acid fragments using the labeled nucleotide; and determining the sequence at the junction of the one or more end joined nucleic acid fragments.

Abstract: Methods for analyzing spatial proximity and epigenetic profile of nucleic acids in cells, the method comprising: fragmenting the nucleic acids, the fragmented nucleic acids comprising overhanging ends; filling in the overhanding ends with one or more labeled nucleotides; joining the filled in ends to create one or more end-joined nucleic acid fragments with one or more junctions; treating the end-joined nucleic acid fragments with bisulfite; isolating the bisulfite-treated end-joined nucleic acid fragments using the label; and determining sequence at the one or more junctions in the bisulfite treated end-joined nucleic acid fragments, thereby determining spatial proximity between the nucleic acids and the methylation profile of the nucleic acids.

Abstract: Embodiments provide a method for sequencing and assembling long DNA genomes comprising generating a 3D contact map of chromatin loop structures in a target genome, the 3D contact map of chromatin loop structures defining spatial proximity relationships between genomic loci in the genome, and deriving a linear genomic nucleic acid sequence from the 3D map of chromatin loop structures

Abstract: Provided herein includes a method for generating an error-corrected genome assembly for an organism comprising: generating a genomic contact map derived from a DNA proximity ligation assay conducted on one or more samples from the organism or a closely related species; superimposing a reference assembled genome derived from whole genome sequencing of one or more samples from the organism on top of the genomic contact map using computer software; correcting errors in the reference assembled genome through a computer user interface to obtain a corrected assembly file, wherein errors in the reference assembled genome are visualized by observing aberrant contacts in the genomic contact map; and applying the corrected assembly file to the reference assembled genome.