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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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The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM