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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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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