We have a eukaryotic diploid genome assembled and scaffolded using ALLPATHS-LG. In addition, we have a linkage map generated from iso-crossing individuals and performing reduced-representation (GBS) sequencing. We have evidence from the linkage map that can place and order our scaffolds, or at times nest a scaffold within a scaffold gap of a larger scaffold, but it would be a lot of work to manual review these joins and investigate mate-pair evidence across the entire genome. I was wondering if there was any existing pipelines or software programs that generate superscaffolded assemblies based off of a mix of linkage map information and mate-pair information. I have seen several papers, but their methods are either not clearly described, or are very manual in nature, but it is likely I could be missing something.
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Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...