Linked-Reads for Haplotype Reconstruction and Improved de novo Assembly
This presentation discusses the challenges of reconstructing genomes, and defines and explains linked-reads. It then explains how linked-reads are generated, beginning with HMW gDNA. Next, it explains how long-range physical coverage is used, as well as high accuracy and long-range haplotype reconstruction. It continues to talk about the supernova for diploid, de novo assembly and discuss how the consistency of the assemblies, the recent improvements, and how plant genes are represented. Finally, it briefly overviews other assembly approaches before summarizing the challenges that would be worked on in the future.
Application of Dovetail's Proximity Ligation Technologies on Challenging Genomes
This presentation describes Dovetail’s integrated solutions; including HMW DNA extraction, library preparation and sequencing, De novo assembly, scaffolding, and gap filling. It then talks about their proximity ligation approaches, as well as how Dovetail differed from Chicago in terms of Hi-C data. Finally, it details how these are used with tetraploid grasses and quinoa.
Assembly and Annotation of Diploid and Polyploid Genomes with PacBio
This presentation introduces PacBio data for genome assembly and its annotation. It then discusses assembly workflow using FALCON-Unzip before talking about the assembly output for complex genomes.
Chromosome-Scale Genome Scaffolding Using Hi-C Data
This presentation explains how chromosomes are formed from contigs using Hi-C. It also discusses how proximity-guided assembly and how it yields chromosome scaffolds. It goes into detail about the different plant genomes this has been successfully used with, including tetraploid and hexaploid plants. Next, it discusses Polar Star and Matlock, and how they are tools for working with chimeric contigs and Hi-C data, respectively. It finishes by explained the Hi-C kit that is now offered by Phase Genomics.
A Comprehensive Suite of Polyploid Genomics Analysis Tools
This presentation discusses NRGene and their genomic Big Data tools, which include De Novo Magic, Pan Magic, and Geno Magic. It talks about how their product portfolio works, as well as the accuracy and cost of the De Novo assembly involved with De Novo Magic. Next, it discusses Pan Magic, and how it works across the pan-genome. Finally, the presentation addresses Geno Magic, and how it works with haplotype databases and genotype imputation.
Annotation of Polyploid Genomes
This presentation discusses the importance of annotation in polyploid genomes. Next, it details the confounding effects of homologous transcript alignment and the concern that it will affect gene prediction. To address this, it discusses the resiliency of gene prediction, as well as structural and functional annotation of genes.
Status of Genomic Approaches in Polyploids Summary and Future Outlook
This presentation begins by identifying several reference genomes for polyploids. This presentation specifically focuses on Fragaria vesca, or the woodland strawberry, and the tandem gene clusters. It wraps up by discussing the future directions of pan-genomes.
Status of Genomic Approaches in Polyploid Crops
This presentation discusses the status of genomic approaches in polyploid crops, specifically the polyploid genome gaps.