Journal: bioRxiv

Article Title: A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

doi: 10.1101/327817

Figure Lengend Snippet: Collinear DLE-1 markers on the two maps are linked (gray lines). All but three chromosomes are captured by two DLS maps. Large inversions on chromosomes 6 and 7 are marked by regions of reversed alignments between the two maps. Regions in green are stretches of random nucleotides in the reference assembly. Regions in yellow exhibit breaks in collinearity between the two maps.

Article Snippet: This study demonstrates that the Oxford Nanopore sequencing technology, combined with the DLS optical mapping technology recently developed by BioNano Genomics, can generate chromosome-scale assemblies of large and repeat-rich plant genomes.

Techniques:

Journal: bioRxiv

Article Title: A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

doi: 10.1101/327817

Figure Lengend Snippet: Left: DLS maps aligning to in-silico maps of Chromosome 6 from public v3.0.1 assembly; Center: Close-up view of DLS map 6 and mapped ONT contigs; Right: Close-up views of hybrid maps (center - green) generated by merging DLS maps (left - blue) and in-silico maps of ONT contigs (“Ctg”, right - blue). Distances are shown, in Mbps.

Article Snippet: This study demonstrates that the Oxford Nanopore sequencing technology, combined with the DLS optical mapping technology recently developed by BioNano Genomics, can generate chromosome-scale assemblies of large and repeat-rich plant genomes.

Techniques: In Silico, Generated

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Methylation states in predicted enhancer–promoter pairs. ( A ) schematic illustration of possible methylation states for a promoter and enhancers, and potential interaction between them. ( B ) Bionano Genomics optical methylation map of a region in chromosome 17 in GM12878 DNA. The region contains the gene TP53, its promoter (small blue box), and several predicted enhancers (pink boxes). Dark blue dots denote unmethylated sites and orange dots denote genetic tags used for alignment to the hg38 reference.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of mixtures containing B-lymphocytes and myoblast cells by different methods using methylation states in promoters alone and enhancer–promoter pairs, accounting for one enhancer per promoter. ( A ) Calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) The mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of B-lymphocytes and myoblast cells mixtures by different methods using methylation states in all predicted enhancer–promoter pairs. ( A ) calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) the mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation